Citrus Sinensis ID: 039644

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190--
Protein Sequence
IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKREKEVWESAIDKLQRILHP
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHccccccccccccHHHccccccHHHHHHHHHHHHHccccccccHHHHHHHHccccEEEEEcccccHHHHHHHHccccccccccEEEEEcccccHHcccccccEEEcccccHHHHHHHHHHHHcccccccccHHHHHHHHHcccccccHHHHHHHcccccccHHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHcccHHHHHHHHHHHcccccHHHHHHHHHHHHHccccHHHHHHHHHHHHcccEEEEEEccccHHHHHHHHHccccccccccEEEEEEccHHHHHHccccEEEEEEcccHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHccccHHHHHHHHHHccccHHHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
IGKTAIARAIFDKISGDFECSCFLEnvreesqrpgglACLRQKLLSNilkdknvmpyidLNFRRLSRMKVLIVFDDVTCFSQLESLmgsldwltpvSRIILTTRNKQVLRNWGVSKIYEMEALEYHHALELFSqhafkrnhpdvgyeklSSNVTKYAQGIPLALKVLSCFLHKREKEVWESAIDKLQRILHP
Flexible Loop (DISEMBL)
igktaiaraifdkisgDFECSCFLENVreesqrpggLACLRQKLLsnilkdknvmpyIDLNFRRLSRMKVLIVFDDVTCFSQLESLmgsldwltPVSRIIlttrnkqvlrnWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKREKEVWESaidklqrilhp
Low Complexity Region (SEG)
IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKREKEVWESAIDKLQRILHP
Disordered region (IsUnstruct)
****AIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKREKEVWESAIDKL******
Disordered Region (DISOPRED)
IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKREKEVWESAIDKLQRIL**
Disordered Region (DISEMBL)
IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKREKEVWESAIDKLQRILHP
Disordered Region (DISPRO)
IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKREKEVWESAIDKLQRILH*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKREKEVWESAIDKLQRILHP
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	192	2.2.26 [Sep-21-2011]
Q40392	1144	TMV resistance protein N	N/A	no	0.947	0.159	0.414	2e-30
O82500	1095	Putative disease resistan	no	no	0.973	0.170	0.367	1e-26
Q9FL92	1372	Probable WRKY transcripti	no	no	0.864	0.120	0.367	5e-24
Q9FKN7	1613	Protein DA1-related 4 OS=	no	no	0.963	0.114	0.364	4e-23
Q9FH83	1288	Probable WRKY transcripti	no	no	0.963	0.143	0.368	3e-22
O23530	1301	Protein SUPPRESSOR OF npr	no	no	0.994	0.146	0.331	3e-21
Q9SZ67	1895	Probable WRKY transcripti	no	no	0.864	0.087	0.321	8e-16
Q9LVT1	623	Putative disease resistan	no	no	0.572	0.176	0.302	4e-07
Q9LZ25	811	Probable disease resistan	no	no	0.609	0.144	0.296	5e-06
Q9SZA7	816	Probable disease resistan	no	no	0.911	0.214	0.260	4e-05

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

 Score =  132 bits (331), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 82/198 (41%), Positives = 117/198 (59%), Gaps = 16/198 (8%)

Query: 1   IGKTAIARAIFDKISG------DFECSCFLENVREESQRPGGLACLRQKLLSNILKDK-N 53
           +GKT IARAIFD + G       F+ +CFL++++E  +   G+  L+  LLS +L++K N
Sbjct: 220 VGKTTIARAIFDTLLGRMDSSYQFDGACFLKDIKENKR---GMHSLQNALLSELLREKAN 276

Query: 54  VMPYIDLNFRRLSRM---KVLIVFDDVTCFSQ-LESLMGSLDWLTPVSRIILTTRNKQVL 109
                D   +  SR+   KVLIV DD+      LE L G LDW    SRII+TTR+K ++
Sbjct: 277 YNNEEDGKHQMASRLRSKKVLIVLDDIDNKDHYLEYLAGDLDWFGNGSRIIITTRDKHLI 336

Query: 110 RNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSC 169
               +  IYE+ AL  H +++LF QHAF +  P+  +EKLS  V  YA+G+PLALKV   
Sbjct: 337 EKNDI--IYEVTALPDHESIQLFKQHAFGKEVPNENFEKLSLEVVNYAKGLPLALKVWGS 394

Query: 170 FLHKREKEVWESAIDKLQ 187
            LH      W+SAI+ ++
Sbjct: 395 LLHNLRLTEWKSAIEHMK 412

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 =  119 bits (298), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 71/193 (36%), Positives = 111/193 (57%), Gaps = 6/193 (3%)

Query: 1   IGKTAIARAIFDKISGDFECSCFLENVREESQRPG----GLAC-LRQKLLSNILKDKNV- 54
           +GKT IARA++++   +F  S F+ENVRE     G    GL   L+Q+ LS +L  K++ 
Sbjct: 216 VGKTTIARALYNQYHENFNLSIFMENVRESYGEAGLDDYGLKLHLQQRFLSKLLDQKDLR 275

Query: 55  MPYIDLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGV 114
           + ++     RL   KVLI+ DDV    QL++L     W    SRI++TT+NKQ+L +  +
Sbjct: 276 VRHLGAIEERLKSQKVLIILDDVDNIEQLKALAKENQWFGNKSRIVVTTQNKQLLVSHDI 335

Query: 115 SKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKR 174
           + +Y++       AL +F QHAFK++ P    + L+   T  A  +PLAL+VL  F+  +
Sbjct: 336 NHMYQVAYPSKQEALTIFCQHAFKQSSPSDDLKHLAIEFTTLAGHLPLALRVLGSFMRGK 395

Query: 175 EKEVWESAIDKLQ 187
            KE WE ++  L+
Sbjct: 396 GKEEWEFSLPTLK 408

Arabidopsis thaliana (taxid: 3702)

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

 Score =  110 bits (276), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 61/166 (36%), Positives = 94/166 (56%)

Query: 1   IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDL 60
           IGKT +A+A+FD++SG+F+  CF+E+  +  Q  G    L ++ L         +  + L
Sbjct: 174 IGKTTLAKAVFDQMSGEFDAHCFIEDYTKAIQEKGVYCLLEEQFLKENAGASGTVTKLSL 233

Query: 61  NFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEM 120
              RL+  +VL+V DDV     +ES +G  DW  P S II+T+++K V R   V++IYE+
Sbjct: 234 LRDRLNNKRVLVVLDDVRSPLVVESFLGGFDWFGPKSLIIITSKDKSVFRLCRVNQIYEV 293

Query: 121 EALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKV 166
           + L    AL+LFS  A   +  +    ++S  V KYA G PLAL +
Sbjct: 294 QGLNEKEALQLFSLCASIDDMAEQNLHEVSMKVIKYANGHPLALNL 339

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

 Score =  107 bits (268), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 70/192 (36%), Positives = 108/192 (56%), Gaps = 7/192 (3%)

Query: 1   IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVM--PYI 58
           IGKT +A+A+F+ +S D++ SCF+EN  E   + G    L++++   ILKD+  +   YI
Sbjct: 200 IGKTTLAKAVFNHMSTDYDASCFIENFDEAFHKEGLHRLLKERI-GKILKDEFDIESSYI 258

Query: 59  ---DLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVS 115
               L+  +L   ++L+V DDV      ES +  LDW    S II+T+ +KQV     ++
Sbjct: 259 MRPTLHRDKLYDKRILVVLDDVRDSLAAESFLKRLDWFGSGSLIIITSVDKQVFAFCQIN 318

Query: 116 KIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKRE 175
           +IY ++ L  H AL+LFSQ  F  N P+    KLS  V  Y  G PLAL +    L  ++
Sbjct: 319 QIYTVQGLNVHEALQLFSQSVFGINEPEQNDRKLSMKVIDYVNGNPLALSIYGRELMGKK 378

Query: 176 KEVWESAIDKLQ 187
            E+ E+A  +L+
Sbjct: 379 SEM-ETAFFELK 389

Arabidopsis thaliana (taxid: 3702)

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

 Score =  104 bits (260), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 70/190 (36%), Positives = 104/190 (54%), Gaps = 5/190 (2%)

Query: 1   IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDL 60
           IGKT +A+A+FD++S  F+ SCF+E+  +     G    L ++LL     D  +M    L
Sbjct: 183 IGKTTLAKAVFDQMSSAFDASCFIEDYDKSIHEKGLYCLLEEQLLPG--NDATIMKLSSL 240

Query: 61  NFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEM 120
              RL+  +VL+V DDV      ES +   DWL P S II+T+R+KQV    G+++IYE+
Sbjct: 241 R-DRLNSKRVLVVLDDVRNALVGESFLEGFDWLGPGSLIIITSRDKQVFCLCGINQIYEV 299

Query: 121 EALEYHHALELFSQHA-FKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKREK-EV 178
           + L    A +LF   A  K +  +   ++LS  V  YA G PLA+ V    L  ++K   
Sbjct: 300 QGLNEKEARQLFLLSASIKEDMGEQNLQELSVRVINYANGNPLAISVYGRELKGKKKLSE 359

Query: 179 WESAIDKLQR 188
            E+A  KL+R
Sbjct: 360 METAFLKLKR 369

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

 Score =  101 bits (252), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 64/193 (33%), Positives = 104/193 (53%), Gaps = 2/193 (1%)

Query: 1   IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQK-LLSNILKDKNV-MPYI 58
           IGK+ I RA++ K+S  F    F+           G+    +K LLS IL  K++ + + 
Sbjct: 216 IGKSTIGRALYSKLSIQFHHRAFITYKSTSGSDVSGMKLRWEKELLSEILGQKDIKIEHF 275

Query: 59  DLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIY 118
            +  +RL + KVLI+ DDV     L++L+G  +W    SRII+ T+++Q+L+   +  IY
Sbjct: 276 GVVEQRLKQQKVLILLDDVDSLEFLKTLVGKAEWFGSGSRIIVITQDRQLLKAHEIDLIY 335

Query: 119 EMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKREKEV 178
           E+E    H AL +  + AF ++ P   +++L+  V K A  +PL L VL   L  R KE 
Sbjct: 336 EVEFPSEHLALTMLCRSAFGKDSPPDDFKELAFEVAKLAGNLPLGLSVLGSSLKGRTKEW 395

Query: 179 WESAIDKLQRILH 191
           W   + +L+  L+
Sbjct: 396 WMEMMPRLRNGLN 408

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

 Score = 83.6 bits (205), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 56/174 (32%), Positives = 100/174 (57%), Gaps = 8/174 (4%)

Query: 1    IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILK-DKNVMPYID 59
            IGKT IA  IF KIS  +E    L+++ +E +  G  A +R+  LS +L+ + +V+   D
Sbjct: 848  IGKTTIAEEIFRKISVQYETCVVLKDLHKEVEVKGHDA-VRENFLSEVLEVEPHVIRISD 906

Query: 60   LNFR----RLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVS 115
            +       RL R ++L++ DDV  +  +++ +G+L++  P SRII+T+RN++V     + 
Sbjct: 907  IKTSFLRSRLQRKRILVILDDVNDYRDVDTFLGTLNYFGPGSRIIMTSRNRRVFVLCKID 966

Query: 116  KIYEMEALEYHHALELFSQHAFKRN-HPDVGYEKLSSNVTKYAQGIPLALKVLS 168
             +YE++ L+   +L L  +   +    P+V Y+ LS  + K++ G P  L+ LS
Sbjct: 967  HVYEVKPLDIPKSLLLLDRGTCQIVLSPEV-YKTLSLELVKFSNGNPQVLQFLS 1019

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|Q9LVT1|DRL39_ARATH Putative disease resistance protein At5g47280 OS=Arabidopsis thaliana GN=At5g47280 PE=3 SV=1

 Score = 54.7 bits (130), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 36/119 (30%), Positives = 60/119 (50%), Gaps = 9/119 (7%)

Query: 71  LIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEMEALEYHHALE 130
           L++ DDV     L+ LM ++    P +  ++ +++K V         Y++E L  H A  
Sbjct: 86  LVILDDVRTRESLDQLMFNI----PGTTTLVVSQSKLV----DPRTTYDVELLNEHDATS 137

Query: 131 LFSQHAFKRNHPDVGYEK-LSSNVTKYAQGIPLALKVLSCFLHKREKEVWESAIDKLQR 188
           LF   AF +     G+ K L   V   ++G+PL+LKVL   L+ R +  W  A+++L R
Sbjct: 138 LFCLSAFNQKSVPSGFSKSLVKQVVGESKGLPLSLKVLGASLNDRPETYWAIAVERLSR 196

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LZ25|DRL30_ARATH Probable disease resistance protein At5g04720 OS=Arabidopsis thaliana GN=At5g04720 PE=2 SV=1

 Score = 50.8 bits (120), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 37/125 (29%), Positives = 63/125 (50%), Gaps = 8/125 (6%)

Query: 65  LSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEMEALE 124
           L   + L++ DDV     L+ LM       P +  ++ +R+K  L +  V+  Y++E L 
Sbjct: 267 LPESRKLVILDDVWTRESLDQLMFEN---IPGTTTLVVSRSK--LADSRVT--YDVELLN 319

Query: 125 YHHALELFSQHAFKRNHPDVGY-EKLSSNVTKYAQGIPLALKVLSCFLHKREKEVWESAI 183
            H A  LF    F +     G+ + L   V    +G+PL+LKV+   L +R ++ WE A+
Sbjct: 320 EHEATALFCLSVFNQKLVPSGFSQSLVKQVVGECKGLPLSLKVIGASLKERPEKYWEGAV 379

Query: 184 DKLQR 188
           ++L R
Sbjct: 380 ERLSR 384

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SZA7|DRL29_ARATH Probable disease resistance protein At4g33300 OS=Arabidopsis thaliana GN=At4g33300 PE=2 SV=3

 Score = 48.1 bits (113), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 50/192 (26%), Positives = 84/192 (43%), Gaps = 17/192 (8%)

Query: 1   IGKTAIARAIFDKISGDFECSCFLEN---VREESQRPGGLACLRQKLLSNILKDKNVMPY 57
           +GKT +A+    ++  D E  C  EN       SQ P  L  LR+ +   +   +   P 
Sbjct: 211 VGKTTLAK----ELQRDHEVQCHFENRILFLTVSQSPL-LEELRELIWGFLSGCEAGNPV 265

Query: 58  IDLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKI 117
            D NF      + L++ DDV     L+ L     +  P    ++ +R+K     +     
Sbjct: 266 PDCNFP-FDGARKLVILDDVWTTQALDRLTS---FKFPGCTTLVVSRSKLTEPKF----T 317

Query: 118 YEMEALEYHHALELFSQHAFKRNHPDVGYEK-LSSNVTKYAQGIPLALKVLSCFLHKREK 176
           Y++E L    A+ LF   AF +    +G+ K L   V    +G+PLALKV    L+ + +
Sbjct: 318 YDVEVLSEDEAISLFCLCAFGQKSIPLGFCKDLVKQVANECKGLPLALKVTGASLNGKPE 377

Query: 177 EVWESAIDKLQR 188
             W+  + +L +
Sbjct: 378 MYWKGVLQRLSK 389

Probable 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	192
392522144	162	NBS-LRR disease resistance protein NBS1,	0.838	0.993	0.552	5e-39
357468659	1160	TIR-NBS-LRR RCT1-like resistance protein	0.984	0.162	0.448	6e-38
147858652	1241	hypothetical protein VITISV_004290 [Viti	0.973	0.150	0.481	7e-38
359493349	1260	PREDICTED: TMV resistance protein N-like	0.973	0.148	0.481	8e-38
255561496	876	TMV resistance protein N, putative [Rici	0.973	0.213	0.497	1e-37
154467307	225	putative NBS-LRR protein, partial [Coffe	0.979	0.835	0.448	2e-37
147768286	1206	hypothetical protein VITISV_033530 [Viti	0.989	0.157	0.474	3e-37
225460354	1174	PREDICTED: TMV resistance protein N-like	0.989	0.161	0.474	5e-37
255564976	944	TMV resistance protein N, putative [Rici	0.958	0.194	0.492	5e-37
449486541	1248	PREDICTED: TMV resistance protein N-like	1.0	0.153	0.436	6e-37

>gi|392522144|gb|AFM77941.1| NBS-LRR disease resistance protein NBS1, partial [Dimocarpus longan]

 Score =  166 bits (420), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 89/161 (55%), Positives = 111/161 (68%)

Query: 1   IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDL 60
           +GKT +A A+F+KI   FE S F  NVREE ++ GGL  LRQKL S +L++KNV     +
Sbjct: 2   VGKTTLAEAVFNKIHRHFEGSYFALNVREEFEQRGGLNSLRQKLHSAVLREKNVDIGTSI 61

Query: 61  NFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEM 120
             RRL R K+LIVFDDVT F Q+E L+GSLD L   SRII+TTR+KQVL N GV  IYE+
Sbjct: 62  GGRRLGRRKLLIVFDDVTDFQQIEYLIGSLDCLGSQSRIIITTRDKQVLNNCGVDCIYEV 121

Query: 121 EALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIP 161
           + L +  ALELF ++ FK+NHP   Y KLS  V  YA G+P
Sbjct: 122 KELIHKDALELFYRYGFKQNHPTADYIKLSKRVLLYAGGLP 162

Source: Dimocarpus longan

Species: Dimocarpus longan

Genus: Dimocarpus

Family: Sapindaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357468659|ref|XP_003604614.1| TIR-NBS-LRR RCT1-like resistance protein [Medicago truncatula] gi|355505669|gb|AES86811.1| TIR-NBS-LRR RCT1-like resistance protein [Medicago truncatula]

 Score =  162 bits (411), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 87/194 (44%), Positives = 124/194 (63%), Gaps = 5/194 (2%)

Query: 1   IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKD-----KNVM 55
           IGKT IA++I++KI  +FE   FLEN+RE  ++  G   L+++L+++ILKD     +++ 
Sbjct: 258 IGKTTIAKSIYNKIGRNFEGRSFLENIREVWEQASGQLYLQERLMNDILKDTTTKIQSIE 317

Query: 56  PYIDLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVS 115
               +   RL   +VLIV DDV    QL +L GS  W  P SRII+TTR+K +LR   V 
Sbjct: 318 SGKSILKERLCHKRVLIVLDDVNKLDQLNALCGSCKWFAPGSRIIITTRDKHILRGKQVD 377

Query: 116 KIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKRE 175
           KIY M+ ++   +LELFS HAFK+  P   + ++S NV KY+ G+PLAL+VL  +L  RE
Sbjct: 378 KIYIMKEMDESESLELFSWHAFKQTRPREDFSEISKNVVKYSAGLPLALEVLGSYLFDRE 437

Query: 176 KEVWESAIDKLQRI 189
              W S +DKL+RI
Sbjct: 438 ILEWRSVLDKLKRI 451

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147858652|emb|CAN82538.1| hypothetical protein VITISV_004290 [Vitis vinifera]

 Score =  162 bits (410), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 91/189 (48%), Positives = 123/189 (65%), Gaps = 2/189 (1%)

Query: 1   IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDL 60
           IGKT +ARAI+++ISG FE  CFL NV   + +  G   LR++LLS +L+DKN+   I  
Sbjct: 287 IGKTTLARAIYEQISGQFEGCCFLPNVEHLASK--GDDYLRKELLSKVLRDKNIDVTITS 344

Query: 61  NFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEM 120
              R    KVLIV D+V   S L++L+G LDW  P SRII+TTR+K VL   GV  IYE+
Sbjct: 345 VKARFHSKKVLIVIDNVNHRSILKTLVGELDWFGPQSRIIITTRDKHVLTMHGVDVIYEV 404

Query: 121 EALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKREKEVWE 180
           + L+   A+ELF+ HAF  + P     +LS  V  YAQG+PLAL+VL   L K+ K+ WE
Sbjct: 405 QKLQDDKAIELFNHHAFINHPPTEDVMELSQRVIAYAQGLPLALEVLGSSLCKKSKDEWE 464

Query: 181 SAIDKLQRI 189
            A++KL++I
Sbjct: 465 CALNKLEKI 473

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359493349|ref|XP_002277814.2| PREDICTED: TMV resistance protein N-like [Vitis vinifera]

 Score =  162 bits (409), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 91/189 (48%), Positives = 123/189 (65%), Gaps = 2/189 (1%)

Query: 1   IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDL 60
           IGKT +ARAI+++ISG FE  CFL NV   + +  G   LR++LLS +L+DKN+   I  
Sbjct: 228 IGKTTLARAIYEQISGQFEGCCFLPNVEHLASK--GDDYLRKELLSKVLRDKNIDVTITS 285

Query: 61  NFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEM 120
              R    KVLIV D+V   S L++L+G LDW  P SRII+TTR+K VL   GV  IYE+
Sbjct: 286 VKARFHSKKVLIVIDNVNHRSILKTLVGELDWFGPQSRIIITTRDKHVLTMHGVDVIYEV 345

Query: 121 EALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKREKEVWE 180
           + L+   A+ELF+ HAF  + P     +LS  V  YAQG+PLAL+VL   L K+ K+ WE
Sbjct: 346 QKLQDDKAIELFNHHAFINHPPTEDVMELSQRVIAYAQGLPLALEVLGSSLCKKSKDEWE 405

Query: 181 SAIDKLQRI 189
            A++KL++I
Sbjct: 406 CALNKLEKI 414

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255561496|ref|XP_002521758.1| TMV resistance protein N, putative [Ricinus communis] gi|223538971|gb|EEF40568.1| TMV resistance protein N, putative [Ricinus communis]

 Score =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 97/195 (49%), Positives = 131/195 (67%), Gaps = 8/195 (4%)

Query: 1   IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV---MPY 57
           IGKT +A AIFD+IS  +E S FL NVRE+ +R   LA LR+KL S IL++KN+    P 
Sbjct: 218 IGKTTLAGAIFDQISAQYESSYFLGNVREQLKR-CLLAELREKLFSKILEEKNLDTRTPN 276

Query: 58  IDLNF--RRLSRMKVLIVFDDVTCFSQLESLM-GSLDWLTPVSRIILTTRNKQVLRNWGV 114
           +   F   RLSR K+L+V DDV    QL+ L+ G  D   P SRII+T+R+KQVL+N  V
Sbjct: 277 LGNTFLKDRLSRKKILVVLDDVDSTMQLQELLPGQHDLFGPGSRIIVTSRDKQVLKNV-V 335

Query: 115 SKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKR 174
            +IY++E L  H AL+LFS +AFK+N P     ++S+ V  YA+G PLAL+VL C L  +
Sbjct: 336 DEIYKVEGLNQHEALQLFSLNAFKKNSPTNDRVEISTRVADYAKGNPLALRVLGCALFDK 395

Query: 175 EKEVWESAIDKLQRI 189
            KE WESA++KL+ +
Sbjct: 396 SKEDWESALEKLRNV 410

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|154467307|gb|ABS82613.1| putative NBS-LRR protein, partial [Coffea canephora]

 Score =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 87/194 (44%), Positives = 127/194 (65%), Gaps = 6/194 (3%)

Query: 1   IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDK-----NVM 55
           IGKT +ARA+FD+IS  FE + FL  VRE S+R G L  L++K+LS IL+ K     NV 
Sbjct: 2   IGKTTLARAVFDRISTHFEGAIFLHEVREHSKRYG-LENLQEKILSEILRIKELRINNVF 60

Query: 56  PYIDLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVS 115
              ++  +RL   KVLIV DD+    QLE+L G  DW    SRII+TT++K +L    + 
Sbjct: 61  EGSNMIKKRLCYKKVLIVLDDIDHLDQLEALAGKHDWFGKGSRIIITTKDKHLLVKHDID 120

Query: 116 KIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKRE 175
           ++Y++E L+ + A++LFS +AFK+N P   YE+LS  +  YA G+PLALK+L  FL+ R+
Sbjct: 121 RMYKVEVLDKYEAVQLFSWNAFKKNCPAKDYEELSLQIVHYAGGLPLALKILGSFLYGRD 180

Query: 176 KEVWESAIDKLQRI 189
              W S +++L++I
Sbjct: 181 MTEWRSEVERLKKI 194

Source: Coffea canephora

Species: Coffea canephora

Genus: Coffea

Family: Rubiaceae

Order: Gentianales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147768286|emb|CAN64759.1| hypothetical protein VITISV_033530 [Vitis vinifera]

 Score =  160 bits (404), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 93/196 (47%), Positives = 122/196 (62%), Gaps = 6/196 (3%)

Query: 1   IGKTAIARAIFDKISGDF-ECSCFLENVREESQRPGGLACLRQKLLSNI----LKDKNVM 55
           IGK+ IA  +++KI   F E  CFL NVREESQR  GLA L+++LLS I    L   N  
Sbjct: 229 IGKSTIAYQVYNKIYAQFDEGYCFLPNVREESQR-HGLAYLQEELLSQISGGNLNKGNFN 287

Query: 56  PYIDLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVS 115
             I+    RL   KVLIV DDV  + QLE L G+ DW    SRII+TT++K +L   GV 
Sbjct: 288 RGINFIKERLHSRKVLIVLDDVDMYEQLEVLAGNHDWFGAGSRIIITTKDKTLLNMHGVD 347

Query: 116 KIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKRE 175
            IY +E L+Y+ AL+LF   AFK + P   Y +L  N  KY +G+PLA+KVL  F+  + 
Sbjct: 348 AIYNVEGLKYNEALKLFCWCAFKHDLPTADYMQLCKNFVKYIEGLPLAIKVLGSFVKNKT 407

Query: 176 KEVWESAIDKLQRILH 191
            + W+SA+DKL+RI H
Sbjct: 408 IDEWKSALDKLKRIPH 423

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225460354|ref|XP_002263146.1| PREDICTED: TMV resistance protein N-like [Vitis vinifera]

 Score =  159 bits (403), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 93/196 (47%), Positives = 122/196 (62%), Gaps = 6/196 (3%)

Query: 1   IGKTAIARAIFDKISGDF-ECSCFLENVREESQRPGGLACLRQKLLSNI----LKDKNVM 55
           IGK+ IA  +++KI   F E  CFL NVREESQR  GLA L+++LLS I    L   N  
Sbjct: 229 IGKSTIAYQVYNKIYAQFDEGYCFLPNVREESQR-HGLAYLQEELLSQISGGNLNKGNFN 287

Query: 56  PYIDLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVS 115
             I+    RL   KVLIV DDV  + QLE L G+ DW    SRII+TT++K +L   GV 
Sbjct: 288 RGINFIKERLHSRKVLIVLDDVDMYEQLEVLAGNHDWFGAGSRIIITTKDKTLLNMHGVD 347

Query: 116 KIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKRE 175
            IY +E L+Y+ AL+LF   AFK + P   Y +L  N  KY +G+PLA+KVL  F+  + 
Sbjct: 348 AIYNVEGLKYNEALKLFCWCAFKHDLPTADYMQLCKNFVKYIEGLPLAIKVLGSFVKNKT 407

Query: 176 KEVWESAIDKLQRILH 191
            + W+SA+DKL+RI H
Sbjct: 408 IDEWKSALDKLKRIPH 423

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  159 bits (402), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 93/189 (49%), Positives = 119/189 (62%), Gaps = 5/189 (2%)

Query: 2   GKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLN 61
           GKT  A  +F++IS  F+  CFL NV EES+R G L   RQ L S +L   NV  Y +  
Sbjct: 225 GKTTTAEVVFNRISTQFDSCCFLANVNEESERYGLLKLQRQ-LFSKLLGQDNV-NYAEGI 282

Query: 62  F--RRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYE 119
           F   RL   KVLIV DDV    QLE+L G  +W  P SRIILT+R+K VL+N     IY+
Sbjct: 283 FDKSRLKHRKVLIVLDDVNNLRQLENLAGEHNWFGPGSRIILTSRDKDVLKN-KTDAIYK 341

Query: 120 MEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKREKEVW 179
           +E L++H AL+LFS +AF++  P   Y KLS  V  YA+G PL LKVL  FL++R  + W
Sbjct: 342 IEDLDHHEALQLFSLNAFRQECPKADYMKLSKRVINYAKGNPLGLKVLGSFLYQRNIKEW 401

Query: 180 ESAIDKLQR 188
           ESA+ KL+R
Sbjct: 402 ESALHKLER 410

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449486541|ref|XP_004157327.1| PREDICTED: TMV resistance protein N-like [Cucumis sativus]

 Score =  159 bits (402), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 86/197 (43%), Positives = 122/197 (61%), Gaps = 5/197 (2%)

Query: 1   IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDK-----NVM 55
           IGKT +A+A+++KI+  FE  CFL NVRE  ++   L  L++KLLS ILKD      NV 
Sbjct: 231 IGKTTLAKALYNKIAYQFEACCFLSNVRETLEQFKDLVQLQEKLLSEILKDNAWKVGNVH 290

Query: 56  PYIDLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVS 115
              ++   RL   KVLI+ DDV    QL++L+G  DW    S+II TTR++ +L N    
Sbjct: 291 KGKNIIRDRLCSKKVLIILDDVDKDEQLDALVGERDWFGRGSKIIATTRDRHLLENHSFD 350

Query: 116 KIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKRE 175
            +Y ++ L+   +LELFS HAFK+NHP   Y  LS     Y +G+PLAL +L   LHKRE
Sbjct: 351 IVYPIQLLDPKKSLELFSLHAFKQNHPSSNYVDLSKFAVSYCKGLPLALVILGSLLHKRE 410

Query: 176 KEVWESAIDKLQRILHP 192
           +++W+S + +L+  L P
Sbjct: 411 RKIWKSKLHELENSLEP 427

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	192
UNIPROTKB|Q40392	1144	N "TMV resistance protein N" [	0.947	0.159	0.414	6.2e-29
TAIR|locus:2129670	1008	AT4G14370 [Arabidopsis thalian	0.989	0.188	0.369	3.3e-27
TAIR|locus:2175991	1294	AT5G17680 [Arabidopsis thalian	0.984	0.146	0.363	1.3e-26
TAIR|locus:2118106	1219	AT4G12010 [Arabidopsis thalian	0.984	0.155	0.403	1.5e-26
TAIR|locus:2195478	1031	AT1G63870 [Arabidopsis thalian	0.989	0.184	0.335	1.1e-25
TAIR|locus:2155801	1046	AT5G58120 [Arabidopsis thalian	0.984	0.180	0.352	1.1e-25
TAIR|locus:2167457	1191	AT5G36930 [Arabidopsis thalian	0.979	0.157	0.395	1.3e-25
TAIR|locus:2136108	1095	AT4G11170 [Arabidopsis thalian	0.973	0.170	0.367	1.5e-25
TAIR|locus:2146243	900	AT5G18360 [Arabidopsis thalian	0.984	0.21	0.386	1.8e-25
TAIR|locus:2195468	1017	AT1G63880 [Arabidopsis thalian	0.984	0.185	0.352	2.2e-25

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

 Score = 334 (122.6 bits), Expect = 6.2e-29, P = 6.2e-29
 Identities = 82/198 (41%), Positives = 117/198 (59%)

Query:     1 IGKTAIARAIFDKISG------DFECSCFLENVREESQRPGGLACLRQKLLSNILKDK-N 53
             +GKT IARAIFD + G       F+ +CFL++++E  +   G+  L+  LLS +L++K N
Sbjct:   220 VGKTTIARAIFDTLLGRMDSSYQFDGACFLKDIKENKR---GMHSLQNALLSELLREKAN 276

Query:    54 VMPYIDLNFRRLSRM---KVLIVFDDVTCFSQ-LESLMGSLDWLTPVSRIILTTRNKQVL 109
                  D   +  SR+   KVLIV DD+      LE L G LDW    SRII+TTR+K ++
Sbjct:   277 YNNEEDGKHQMASRLRSKKVLIVLDDIDNKDHYLEYLAGDLDWFGNGSRIIITTRDKHLI 336

Query:   110 RNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSC 169
                 +  IYE+ AL  H +++LF QHAF +  P+  +EKLS  V  YA+G+PLALKV   
Sbjct:   337 EKNDI--IYEVTALPDHESIQLFKQHAFGKEVPNENFEKLSLEVVNYAKGLPLALKVWGS 394

Query:   170 FLHKREKEVWESAIDKLQ 187
              LH      W+SAI+ ++
Sbjct:   395 LLHNLRLTEWKSAIEHMK 412

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2129670 AT4G14370 [Arabidopsis thaliana (taxid:3702)]

 Score = 317 (116.6 bits), Expect = 3.3e-27, P = 3.3e-27
 Identities = 72/195 (36%), Positives = 108/195 (55%)

Query:     1 IGKTAIARAIFDKISGDFECSCFLENVREESQRP----GGLACLRQKLLSNILKDKNVMP 56
             IGKT IARA++  +   F+ SCF+EN+     R     G    L+++LLS IL    +  
Sbjct:   177 IGKTTIARALYSLLLSSFQLSCFVENLSGSDNRGLDEYGFKLRLQEQLLSKILNQNGMRI 236

Query:    57 Y-IDLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVS 115
             Y +     RL   KVLIV DDV    QLE+L     W  P SRII+TT +K +L   G++
Sbjct:   237 YHLGAIQERLCDQKVLIVLDDVNDLKQLEALANETSWFGPGSRIIVTTEDKGLLEQHGIN 296

Query:   116 KIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKRE 175
             K Y +       ALE+F  +AF+++ P  G++KL+  VT     +PL L+V+   L  + 
Sbjct:   297 KTYHVGFPSIEEALEIFCIYAFRKSSPPDGFKKLTKRVTNVFDNLPLGLRVMGSSLRGKG 356

Query:   176 KEVWESAIDKLQRIL 190
             ++ WE+ +D+L+  L
Sbjct:   357 EDEWEALLDRLETSL 371

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;ISS

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

GO:0043531 "ADP binding" evidence=IEA

GO:0035091 "phosphatidylinositol binding" evidence=ISS

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

 Score = 313 (115.2 bits), Expect = 1.3e-26, P = 1.3e-26
 Identities = 72/198 (36%), Positives = 113/198 (57%)

Query:     1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNIL--KDKNVMPYI 58
             +GKT IA+ +++++SG F+  CF+ENV+E   R G +  L+ + L  +   +DK     +
Sbjct:   217 VGKTTIAKYLYNQLSGQFQVHCFMENVKEVCNRYG-VRRLQVEFLCRMFQERDKEAWSSV 275

Query:    59 DL-NF--RRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVS 115
                N    R     V IV DDV    QL  L+    W  P SRII+TTR++ +L + G++
Sbjct:   276 SCCNIIKERFRHKMVFIVLDDVDRSEQLNELVKETGWFGPGSRIIVTTRDRHLLLSHGIN 335

Query:   116 KIYEMEALEYHHALELFSQHAFKRNH--PDVGYEKLSSNVTKYAQGIPLALKVLSCFLHK 173
              +Y+++ L    AL+LF  +AF+     P  G+E+LS     YA G+PLAL+VL  FL++
Sbjct:   336 LVYKVKCLPKKEALQLFCNYAFREEIILPH-GFEELSVQAVNYASGLPLALRVLGSFLYR 394

Query:   174 REKEVWESAIDKLQRILH 191
             R +  WES + +L+   H
Sbjct:   395 RSQIEWESTLARLKTYPH 412

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 = 312 (114.9 bits), Expect = 1.5e-26, P = 1.5e-26
 Identities = 79/196 (40%), Positives = 112/196 (57%)

Query:     1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDL 60
             IGKT +A  ++ ++ G F+ SCFL N+RE S R  GL  L QKL S +L D+++      
Sbjct:   220 IGKTTLADCLYGRMRGQFDGSCFLTNIRENSGR-SGLESLLQKLFSTVLNDRDLEIGAPG 278

Query:    61 N----F-RRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVS 115
             N    F RRL   ++LIV DDV    Q+  LMG   W    SRII+TTR+ +++      
Sbjct:   279 NAHERFERRLKSKRLLIVLDDVNDEKQIRYLMGHCKWYQGGSRIIITTRDSKLIETIKGR 338

Query:   116 KIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKRE 175
             K Y +  L    AL+LFS +AF  + P   +E L++ V  YA+G PLALKVL   L +R+
Sbjct:   339 K-YVLPKLNDREALKLFSLNAFSNSFPLKEFEGLTNMVLDYAKGHPLALKVLGSDLCERD 397

Query:   176 KEVWESAIDKLQRILH 191
                WE+ +D+L+   H
Sbjct:   398 DLYWEAKLDRLKSRSH 413

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:2195478 AT1G63870 [Arabidopsis thaliana (taxid:3702)]

 Score = 303 (111.7 bits), Expect = 1.1e-25, P = 1.1e-25
 Identities = 64/191 (33%), Positives = 108/191 (56%)

Query:     1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV-MPYID 59
             IGKT IARA+  ++S  F+ +CF++N++E          L+++ L+ +L    + + +  
Sbjct:   222 IGKTTIARALQSRLSNKFQLTCFVDNLKESFLNSLDELRLQEQFLAKVLNHDGIRICHSG 281

Query:    60 LNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYE 119
             +   RL + +VLI+ DDV    QLE+L     W    SRI++TT NK++L+  G++ +Y 
Sbjct:   282 VIEERLCKQRVLIILDDVNHIMQLEALANETTWFGSGSRIVVTTENKEILQQHGINDLYH 341

Query:   120 MEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKREKEVW 179
             +       A E+  ++AF++     G+EKL+  VTK    +PL L+VL   L  + +E W
Sbjct:   342 VGFPSDEQAFEILCRYAFRKTTLSHGFEKLARRVTKLCGNLPLGLRVLGSSLRGKNEEEW 401

Query:   180 ESAIDKLQRIL 190
             E  I +L+ IL
Sbjct:   402 EEVIRRLETIL 412

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:2155801 AT5G58120 [Arabidopsis thaliana (taxid:3702)]

 Score = 303 (111.7 bits), Expect = 1.1e-25, P = 1.1e-25
 Identities = 69/196 (35%), Positives = 112/196 (57%)

Query:     1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPG----GLAC-LRQKLLSNILKDKNV- 54
             IGKT IARA+  ++S  F+ +CF+EN+R  S   G    GL   L+++LLS +L    + 
Sbjct:   221 IGKTTIARALHSRLSSSFQLTCFMENIRG-SYNSGLDEYGLKLRLQEQLLSKVLNHDGIR 279

Query:    55 MPYIDLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGV 114
             + ++     RL   KVLI+ DDV    QLE+L    +W  P SRII+TT ++++L    V
Sbjct:   280 INHLGAIPERLCDQKVLIILDDVDDLQQLEALANETNWFGPGSRIIVTTEDQELLEQHDV 339

Query:   115 SKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKR 174
             +K Y ++      A ++F  +AF+R+    G+EKL+  VT     +PL L+V+   L  +
Sbjct:   340 NKKYHVDFPTREEACKIFCTYAFRRSFAPYGFEKLAERVTWLCSNLPLGLRVMGSTLRGK 399

Query:   175 EKEVWESAIDKLQRIL 190
             +++ WE  + +L+  L
Sbjct:   400 KEDDWEGILRRLENSL 415

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

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

GO:0007165 "signal transduction" evidence=IEA

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2167457 AT5G36930 [Arabidopsis thaliana (taxid:3702)]

 Score = 303 (111.7 bits), Expect = 1.3e-25, P = 1.3e-25
 Identities = 76/192 (39%), Positives = 108/192 (56%)

Query:     1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDL 60
             IGKT +A+  F++ S  FE S FLEN RE S++P G   L+ +LLS+IL+ +N + +  L
Sbjct:   223 IGKTTLAKVAFNEFSHLFEGSSFLENFREYSKKPEGRTHLQHQLLSDILR-RNDIEFKGL 281

Query:    61 NF---RRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKI 117
             +     R    +VL+V DDV    QL S     D     SRII+TTRN  +L+       
Sbjct:   282 DHAVKERFRSKRVLLVVDDVDDVHQLNSAAIDRDCFGHGSRIIITTRNMHLLKQLRAEGS 341

Query:   118 YEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKREKE 177
             Y  + L+   +LELFS HAF+ + P   + + S  V  Y  G+PLA++VL  FL +R   
Sbjct:   342 YSPKELDGDESLELFSWHAFRTSEPPKEFLQHSEEVVTYCAGLPLAVEVLGAFLIERSIR 401

Query:   178 VWESAIDKLQRI 189
              WES +  L+RI
Sbjct:   402 EWESTLKLLKRI 413

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0007165 "signal transduction" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 302 (111.4 bits), Expect = 1.5e-25, P = 1.5e-25
 Identities = 71/193 (36%), Positives = 111/193 (57%)

Query:     1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPG----GLAC-LRQKLLSNILKDKNV- 54
             +GKT IARA++++   +F  S F+ENVRE     G    GL   L+Q+ LS +L  K++ 
Sbjct:   216 VGKTTIARALYNQYHENFNLSIFMENVRESYGEAGLDDYGLKLHLQQRFLSKLLDQKDLR 275

Query:    55 MPYIDLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGV 114
             + ++     RL   KVLI+ DDV    QL++L     W    SRI++TT+NKQ+L +  +
Sbjct:   276 VRHLGAIEERLKSQKVLIILDDVDNIEQLKALAKENQWFGNKSRIVVTTQNKQLLVSHDI 335

Query:   115 SKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKR 174
             + +Y++       AL +F QHAFK++ P    + L+   T  A  +PLAL+VL  F+  +
Sbjct:   336 NHMYQVAYPSKQEALTIFCQHAFKQSSPSDDLKHLAIEFTTLAGHLPLALRVLGSFMRGK 395

Query:   175 EKEVWESAIDKLQ 187
              KE WE ++  L+
Sbjct:   396 GKEEWEFSLPTLK 408

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:2146243 AT5G18360 [Arabidopsis thaliana (taxid:3702)]

 Score = 300 (110.7 bits), Expect = 1.8e-25, P = 1.8e-25
 Identities = 77/199 (38%), Positives = 120/199 (60%)

Query:     1 IGKTAIARAIFDKISGDFECSCFLENVREESQRP-----GGLACLRQKLLSNILKDKNVM 55
             IGKT IARA+F+++S +F+ + F+ENV+  S+       G    L+++ LS ++  K+ M
Sbjct:   218 IGKTTIARALFNRLSENFQHTIFMENVKGSSRTSELDAYGFQLRLQEQFLSEVIDHKH-M 276

Query:    56 PYIDLNF--RRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWG 113
                DL     RL  +KVL+V DDV    QL++L+    W    SRII+TT NKQ+LR  G
Sbjct:   277 KIHDLGLVKERLQDLKVLVVLDDVDKLEQLDALVKQSQWFGSGSRIIVTTENKQLLRAHG 336

Query:   114 VSKIYEMEALEYHHALELFSQHAF-KRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLH 172
             ++ IYE+       +L++F Q+AF + + PD G  +L++ +TK A  +PLALKVL   L 
Sbjct:   337 ITCIYELGFPSRSDSLQIFCQYAFGESSAPD-GCIELATEITKLAGYLPLALKVLGSSLR 395

Query:   173 KREKEVWESAIDKLQRILH 191
                K+  +SA+ +L+  L+
Sbjct:   396 GMSKDEQKSALPRLRTSLN 414

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

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

GO:0007165 "signal transduction" evidence=IEA

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2195468 AT1G63880 [Arabidopsis thaliana (taxid:3702)]

 Score = 300 (110.7 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 69/196 (35%), Positives = 111/196 (56%)

Query:     1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPG----GLAC-LRQKLLSNILKDKNV- 54
             IGKT IARA++  +S  F+ SCF++N+R  S   G    G    L+++ LS +L    + 
Sbjct:   219 IGKTTIARALYGLLSKRFQLSCFVDNLRG-SYHSGFDEYGFKLHLQEQFLSKVLNQSGMR 277

Query:    55 MPYIDLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGV 114
             + ++      LS  +VLI+ DDV    QLE+L     W  P SRI++TT NK++L+  G+
Sbjct:   278 ICHLGAIKENLSDQRVLIILDDVNKLKQLEALANETTWFGPGSRIVVTTENKELLQQHGI 337

Query:   115 SKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKR 174
             +  Y +       AL++   +AFK+  P  G+E+LS +VTK    +PL L V+   L  +
Sbjct:   338 NNTYHVGFPSDEDALKILCSYAFKQTSPRHGFEELSESVTKLCGKLPLGLCVVGSSLRGK 397

Query:   175 EKEVWESAIDKLQRIL 190
             +++ WE  + +L+ IL
Sbjct:   398 KEDEWEDVVTRLETIL 413

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

GO:0050832 "defense response to fungus" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00021883001 SubName- Full=Chromosome chr18 scaffold_24, whole genome shotgun sequence; (540 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	192
PLN03210	1153	PLN03210, PLN03210, Resistant to P	1e-28
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	3e-21

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

 Score =  111 bits (278), Expect = 1e-28
 Identities = 71/201 (35%), Positives = 105/201 (52%), Gaps = 11/201 (5%)

Query: 1   IGKTAIARAIFDKISGDFECSCFLENVR-EESQRPGGLAC---------LRQKLLSNILK 50
           IGKT IARA+F ++S  F+ S F++     +S      A          L++  LS IL 
Sbjct: 218 IGKTTIARALFSRLSRQFQSSVFIDRAFISKSMEIYSSANPDDYNMKLHLQRAFLSEILD 277

Query: 51  DKNV-MPYIDLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVL 109
            K++ + ++     RL   KVLI  DD+     L++L G   W    SRII+ T++K  L
Sbjct: 278 KKDIKIYHLGAMEERLKHRKVLIFIDDLDDQDVLDALAGQTQWFGSGSRIIVITKDKHFL 337

Query: 110 RNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSC 169
           R  G+  IYE+       ALE+F + AFK+N P  G+ +L+S V   A  +PL L VL  
Sbjct: 338 RAHGIDHIYEVCLPSNELALEMFCRSAFKKNSPPDGFMELASEVALRAGNLPLGLNVLGS 397

Query: 170 FLHKREKEVWESAIDKLQRIL 190
           +L  R+KE W   + +L+  L
Sbjct: 398 YLRGRDKEDWMDMLPRLRNGL 418

syringae 6; Provisional. Length = 1153

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

 Score = 87.8 bits (218), Expect = 3e-21
 Identities = 53/203 (26%), Positives = 96/203 (47%), Gaps = 20/203 (9%)

Query: 1   IGKTAIARAIFDK--ISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYI 58
           +GKT +A+ I++   + G F+   ++   +  ++         QK +   L   +   ++
Sbjct: 30  VGKTTLAKQIYNDDSVGGHFDSVAWVVVSKTYTE------FRLQKDILQELGLDD-SDWV 82

Query: 59  DLN--------FRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLR 110
           + N           L R + L+V DDV   +  + +          SR+I+TTR++ V  
Sbjct: 83  EKNESELAVKIKEALLRKRFLLVLDDVWEKNDWDKIGVPFPDGENGSRVIVTTRSESVAG 142

Query: 111 NWGV-SKIYEMEALEYHHALELFSQHAFKRNHP-DVGYEKLSSNVTKYAQGIPLALKVLS 168
             G  SK +E+E+LE   + ELFS   F++  P     E+++  + +  +G+PLALKVL 
Sbjct: 143 RMGGTSKPHEVESLEPEESWELFSNKVFEKELPPCPELEEVAKEIVEKCKGLPLALKVLG 202

Query: 169 CFL-HKREKEVWESAIDKLQRIL 190
             L  K   + WE  +++L   L
Sbjct: 203 GLLAFKSTVQEWEHVLEQLNNEL 225

Length = 285

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	192
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	100.0
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.97
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	99.05
PRK04841	903	transcriptional regulator MalT; Provisional	98.97
PF05729	166	NACHT: NACHT domain	98.95
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.77
PF13173	128	AAA_14: AAA domain	98.64
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.54
PRK06893	229	DNA replication initiation factor; Validated	98.53
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.44
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	98.37
COG3903	414	Predicted ATPase [General function prediction only	98.3
PF14516	331	AAA_35: AAA-like domain	98.28
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	98.21
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.21
PRK14087	450	dnaA chromosomal replication initiation protein; P	98.2
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.13
PRK13342	413	recombination factor protein RarA; Reviewed	98.12
PRK05564	313	DNA polymerase III subunit delta'; Validated	98.12
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	98.11
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	98.1
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	98.08
PRK08727	233	hypothetical protein; Validated	98.05
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	98.03
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.96
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	97.95
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.95
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	97.92
PRK09087	226	hypothetical protein; Validated	97.91
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	97.89
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	97.87
PRK08084	235	DNA replication initiation factor; Provisional	97.87
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	97.86
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	97.85
PRK05642	234	DNA replication initiation factor; Validated	97.84
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	97.83
PRK05707	328	DNA polymerase III subunit delta'; Validated	97.82
PRK04132	846	replication factor C small subunit; Provisional	97.82
PRK07471	365	DNA polymerase III subunit delta'; Validated	97.82
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.81
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	97.8
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.8
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.78
PRK07940	394	DNA polymerase III subunit delta'; Validated	97.77
PLN03025	319	replication factor C subunit; Provisional	97.77
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.77
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.75
PRK12402	337	replication factor C small subunit 2; Reviewed	97.75
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.74
PRK09376	416	rho transcription termination factor Rho; Provisio	97.73
PRK09112	351	DNA polymerase III subunit delta'; Validated	97.72
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.71
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.64
PRK14086	617	dnaA chromosomal replication initiation protein; P	97.63
PRK04195	482	replication factor C large subunit; Provisional	97.63
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.63
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.61
COG0593	408	DnaA ATPase involved in DNA replication initiation	97.59
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	97.58
cd01128	249	rho_factor Transcription termination factor rho is	97.57
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.54
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	97.53
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	97.53
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	97.51
PRK08116	268	hypothetical protein; Validated	97.51
PRK12422	445	chromosomal replication initiation protein; Provis	97.49
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.46
PRK13341	725	recombination factor protein RarA/unknown domain f	97.45
KOG2028	554	consensus ATPase related to the helicase subunit o	97.44
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	97.39
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	97.36
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	97.36
TIGR00767	415	rho transcription termination factor Rho. Members	97.34
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	97.32
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	97.3
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	97.3
PRK08769	319	DNA polymerase III subunit delta'; Validated	97.23
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.2
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.15
PTZ00112	1164	origin recognition complex 1 protein; Provisional	97.13
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	97.1
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	97.09
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	97.02
PRK06620	214	hypothetical protein; Validated	97.0
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	96.99
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	96.97
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	96.96
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	96.95
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	96.94
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	96.93
PF00004	132	AAA: ATPase family associated with various cellula	96.92
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	96.91
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	96.9
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	96.83
PHA02544	316	44 clamp loader, small subunit; Provisional	96.81
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	96.8
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	96.77
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	96.75
PRK03992	389	proteasome-activating nucleotidase; Provisional	96.74
PRK08181	269	transposase; Validated	96.69
PRK06090	319	DNA polymerase III subunit delta'; Validated	96.69
PRK07399	314	DNA polymerase III subunit delta'; Validated	96.66
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	96.65
COG3899	849	Predicted ATPase [General function prediction only	96.63
PRK06871	325	DNA polymerase III subunit delta'; Validated	96.61
PRK07993	334	DNA polymerase III subunit delta'; Validated	96.57
CHL00176	638	ftsH cell division protein; Validated	96.55
CHL00181	287	cbbX CbbX; Provisional	96.52
PRK08058	329	DNA polymerase III subunit delta'; Validated	96.51
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	96.51
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	96.46
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	96.44
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	96.43
PRK12608	380	transcription termination factor Rho; Provisional	96.32
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	96.28
PRK12377	248	putative replication protein; Provisional	96.24
PRK06964	342	DNA polymerase III subunit delta'; Validated	96.14
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	96.11
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.11
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	96.11
PRK09183	259	transposase/IS protein; Provisional	96.09
PRK06921	266	hypothetical protein; Provisional	95.97
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	95.92
smart00382	148	AAA ATPases associated with a variety of cellular	95.88
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	95.84
PRK06835	329	DNA replication protein DnaC; Validated	95.69
PRK06526	254	transposase; Provisional	95.67
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	95.66
PRK08939	306	primosomal protein DnaI; Reviewed	95.53
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	95.53
PRK08699	325	DNA polymerase III subunit delta'; Validated	95.45
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	95.4
PRK07952	244	DNA replication protein DnaC; Validated	95.4
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	95.31
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	95.24
CHL00095	821	clpC Clp protease ATP binding subunit	95.23
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	95.22
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	95.2
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	95.15
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	95.12
CHL00195	489	ycf46 Ycf46; Provisional	94.91
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	94.67
PRK10865	857	protein disaggregation chaperone; Provisional	94.62
COG1484	254	DnaC DNA replication protein [DNA replication, rec	94.54
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	94.42
PRK10536	262	hypothetical protein; Provisional	94.38
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	94.33
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	94.19
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	94.02
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	93.96
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	93.89
PRK07276	290	DNA polymerase III subunit delta'; Validated	93.81
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	93.79
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	93.62
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	93.51
PRK08118	167	topology modulation protein; Reviewed	93.38
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	93.28
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	93.24
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	93.07
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	92.65
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	92.65
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	92.46
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	92.46
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	92.27
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	92.25
TIGR02237	209	recomb_radB DNA repair and recombination protein R	92.2
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	92.13
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	92.03
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	92.0
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	91.99
PRK04296	190	thymidine kinase; Provisional	91.98
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	91.91
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	91.75
COG5635	824	Predicted NTPase (NACHT family) [Signal transducti	91.75
PRK12678	672	transcription termination factor Rho; Provisional	91.5
PHA00729	226	NTP-binding motif containing protein	91.37
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	91.34
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	91.24
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	91.12
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	91.1
PRK00409	782	recombination and DNA strand exchange inhibitor pr	91.09
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	91.07
PRK05541	176	adenylylsulfate kinase; Provisional	91.05
cd00983	325	recA RecA is a bacterial enzyme which has roles in	91.04
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	91.03
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	90.7
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	90.6
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	90.51
PTZ00202	550	tuzin; Provisional	90.49
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	90.45
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	90.43
COG1158	422	Rho Transcription termination factor [Transcriptio	90.42
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	90.3
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	90.29
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	90.27
cd01394	218	radB RadB. The archaeal protein radB shares simila	90.19
PF00154	322	RecA: recA bacterial DNA recombination protein; In	90.13
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	90.09
PRK10865	857	protein disaggregation chaperone; Provisional	90.08
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	90.06
PRK09354	349	recA recombinase A; Provisional	89.82
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	89.78
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	89.75
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	89.65
KOG1514	767	consensus Origin recognition complex, subunit 1, a	89.61
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	89.42
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	89.37
PRK04301	317	radA DNA repair and recombination protein RadA; Va	89.34
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	89.29
PRK06762	166	hypothetical protein; Provisional	88.9
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	88.48
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	88.35
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	88.32
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	88.31
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	88.09
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	88.04
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	88.02
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	87.97
PRK07261	171	topology modulation protein; Provisional	87.9
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	86.86
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	86.83
TIGR03324	497	alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit a	86.69
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	86.64
PRK06217	183	hypothetical protein; Validated	86.56
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	86.53
CHL00095	821	clpC Clp protease ATP binding subunit	86.41
PF07726	131	AAA_3: ATPase family associated with various cellu	86.3
PF02572	172	CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase	86.28
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	86.16
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	86.14
CHL00060	494	atpB ATP synthase CF1 beta subunit	85.84
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	85.67
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	85.65
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	85.4
TIGR02236	310	recomb_radA DNA repair and recombination protein R	85.34
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	85.22
cd03216	163	ABC_Carb_Monos_I This family represents the domain	85.15
PTZ00035	337	Rad51 protein; Provisional	85.05
PRK05922	434	type III secretion system ATPase; Validated	84.99
PRK08149	428	ATP synthase SpaL; Validated	84.96
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	84.96
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	84.94
TIGR03496	411	FliI_clade1 flagellar protein export ATPase FliI.	84.94
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	84.82
KOG2383	467	consensus Predicted ATPase [General function predi	84.79
COG2884	223	FtsE Predicted ATPase involved in cell division [C	84.53
PRK11823	446	DNA repair protein RadA; Provisional	84.4
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	84.35
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	84.18
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	83.95
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	83.93
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	83.69
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	83.63
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	83.49
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	83.46
cd01134	369	V_A-ATPase_A V/A-type ATP synthase catalytic subun	83.41
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	83.38
PF06144	172	DNA_pol3_delta: DNA polymerase III, delta subunit;	83.29
PTZ00301	210	uridine kinase; Provisional	83.28
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	83.14
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	83.09
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	82.97
COG0125	208	Tmk Thymidylate kinase [Nucleotide transport and m	82.88
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	82.87
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	82.78
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	82.61
PRK05917	290	DNA polymerase III subunit delta'; Validated	82.55
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	82.51
PRK09281	502	F0F1 ATP synthase subunit alpha; Validated	82.49
PRK07413	382	hypothetical protein; Validated	82.38
TIGR03498	418	FliI_clade3 flagellar protein export ATPase FliI.	82.25
CHL00059	485	atpA ATP synthase CF1 alpha subunit	82.17
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	82.1
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	81.87
PF02463	220	SMC_N: RecF/RecN/SMC N terminal domain; InterPro:	81.82
PF01202	158	SKI: Shikimate kinase; InterPro: IPR000623 Shikima	81.53
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	81.49
PRK09099	441	type III secretion system ATPase; Provisional	81.38
COG1485	367	Predicted ATPase [General function prediction only	81.27
PF07931	174	CPT: Chloramphenicol phosphotransferase-like prote	81.14
PRK08233	182	hypothetical protein; Provisional	80.95
PTZ00185	574	ATPase alpha subunit; Provisional	80.85
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	80.84
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	80.66
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	80.62
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	80.61
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	80.55
COG1763	161	MobB Molybdopterin-guanine dinucleotide biosynthes	80.45
PF02223	186	Thymidylate_kin: Thymidylate kinase; InterPro: IPR	80.31
COG3172	187	NadR Predicted ATPase/kinase involved in NAD metab	80.22
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	80.16
PRK07132	299	DNA polymerase III subunit delta'; Validated	80.12
PRK10867	433	signal recognition particle protein; Provisional	80.12
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	80.04

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=6.8e-33  Score=237.45  Aligned_cols=184  Identities=24%  Similarity=0.336  Sum_probs=164.8

Q ss_pred             CchhHHHHHHHHH---hhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-c-----CchHHHHhhcCCceEE
Q 039644            1 IGKTAIARAIFDK---ISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV-M-----PYIDLNFRRLSRMKVL   71 (192)
Q Consensus         1 iGKTtLa~~~~~~---~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~-----~~~~~l~~~l~~~~~L   71 (192)
                      +||||||++++++   ++.+|+.++|+.+..+     ++..+++.+++..++...+. .     +....+.+.|+.+|||
T Consensus       190 vGKTTL~~qi~N~~~~v~~~Fd~~iWV~VSk~-----f~~~~iq~~Il~~l~~~~~~~~~~~~~~~~~~i~~~L~~krfl  264 (889)
T KOG4658|consen  190 VGKTTLARQIFNKFDEVGNHFDGVIWVVVSKE-----FTTRKIQQTILERLGLLDEEWEDKEEDELASKLLNLLEGKRFL  264 (889)
T ss_pred             ccHHHHHHHHhcccchhcccCceEEEEEEccc-----ccHHhHHHHHHHHhccCCcccchhhHHHHHHHHHHHhccCceE
Confidence            6999999999993   7899999999995443     89999999999988764443 1     2778899999999999


Q ss_pred             EEEeCCCCchhHHHhhccCCCCCCCceEEEEecchhHHhh-cCCCceEecCCCCHHHHHHHHHHhhcCCC-CCCccHHHH
Q 039644           72 IVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRN-WGVSKIYEMEALEYHHALELFSQHAFKRN-HPDVGYEKL  149 (192)
Q Consensus        72 lVlDdv~~~~~~~~l~~~~~~~~~~~~iivTtR~~~~~~~-~~~~~~~~l~~l~~~ea~~lf~~~~~~~~-~~~~~~~~~  149 (192)
                      |||||+|+..+|+.+...+|...+||+|++|||++.++.. ++....++++.|+.+|||.||.+.++... ...+.+.++
T Consensus       265 lvLDDIW~~~dw~~I~~~~p~~~~g~KvvlTTRs~~V~~~~m~~~~~~~v~~L~~~eaW~LF~~~v~~~~~~~~~~i~~l  344 (889)
T KOG4658|consen  265 LVLDDIWEEVDWDKIGVPFPSRENGSKVVLTTRSEEVCGRAMGVDYPIEVECLTPEEAWDLFQKKVGPNTLGSHPDIEEL  344 (889)
T ss_pred             EEEecccccccHHhcCCCCCCccCCeEEEEEeccHhhhhccccCCccccccccCccccHHHHHHhhccccccccccHHHH
Confidence            9999999999999999999988889999999999999999 78888999999999999999999998764 445668999


Q ss_pred             HHHHHHHhCCCchHHHHHHHHhccCC-HHHHHHHHHHHHhc
Q 039644          150 SSNVTKYAQGIPLALKVLSCFLHKRE-KEVWESAIDKLQRI  189 (192)
Q Consensus       150 ~~~i~~~~~g~Plai~~~~~~l~~~~-~~~w~~~l~~l~~~  189 (192)
                      +++++++|+|+|||+.++|+.|+.+. +.+|+++...+...
T Consensus       345 ak~v~~kC~GLPLAl~viG~~ma~K~t~~eW~~~~~~l~s~  385 (889)
T KOG4658|consen  345 AKEVAEKCGGLPLALNVLGGLLACKKTVQEWRRALNVLKSS  385 (889)
T ss_pred             HHHHHHHhCChHHHHHHHHHHhcCCCcHHHHHHHHcccccc
Confidence            99999999999999999999999987 88999999988654

>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=2.5e-33  Score=215.83  Aligned_cols=185  Identities=29%  Similarity=0.448  Sum_probs=144.2

Q ss_pred             CchhHHHHHHHHH--hhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-------cCchHHHHhhcCCceEE
Q 039644            1 IGKTAIARAIFDK--ISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV-------MPYIDLNFRRLSRMKVL   71 (192)
Q Consensus         1 iGKTtLa~~~~~~--~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-------~~~~~~l~~~l~~~~~L   71 (192)
                      +||||||.+++++  ++.+|+.++|+...+.     .+...++..++.++......       .+....+.+.+.++++|
T Consensus        30 ~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~-----~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~~~~L  104 (287)
T PF00931_consen   30 IGKTTLARQVARDLRIKNRFDGVIWVSLSKN-----PSLEQLLEQILRQLGEPDSSISDPKDIEELQDQLRELLKDKRCL  104 (287)
T ss_dssp             SSHHHHHHHHHCHHHHCCCCTEEEEEEEES------SCCHHHHHHHHHHHTCC-STSSCCSSHHHHHHHHHHHHCCTSEE
T ss_pred             CCcceeeeecccccccccccccccccccccc-----cccccccccccccccccccccccccccccccccchhhhccccce
Confidence            6999999999997  8999999999985444     56688999999999876321       22788899999999999


Q ss_pred             EEEeCCCCchhHHHhhccCCCCCCCceEEEEecchhHHhhcCC-CceEecCCCCHHHHHHHHHHhhcCCC-CCCccHHHH
Q 039644           72 IVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGV-SKIYEMEALEYHHALELFSQHAFKRN-HPDVGYEKL  149 (192)
Q Consensus        72 lVlDdv~~~~~~~~l~~~~~~~~~~~~iivTtR~~~~~~~~~~-~~~~~l~~l~~~ea~~lf~~~~~~~~-~~~~~~~~~  149 (192)
                      |||||+|+...|+.+...++....+++||+|||+..++...+. ...+++++|+.++|++||.+.++... .+.....+.
T Consensus       105 lVlDdv~~~~~~~~l~~~~~~~~~~~kilvTTR~~~v~~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~  184 (287)
T PF00931_consen  105 LVLDDVWDEEDLEELREPLPSFSSGSKILVTTRDRSVAGSLGGTDKVIELEPLSEEEALELFKKRAGRKESESPEDLEDL  184 (287)
T ss_dssp             EEEEEE-SHHHH-------HCHHSS-EEEEEESCGGGGTTHHSCEEEEECSS--HHHHHHHHHHHHTSHS----TTSCTH
T ss_pred             eeeeeecccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            9999999999998888777776789999999999988776643 67899999999999999999987655 334556678


Q ss_pred             HHHHHHHhCCCchHHHHHHHHhccCC-HHHHHHHHHHHHhcC
Q 039644          150 SSNVTKYAQGIPLALKVLSCFLHKRE-KEVWESAIDKLQRIL  190 (192)
Q Consensus       150 ~~~i~~~~~g~Plai~~~~~~l~~~~-~~~w~~~l~~l~~~~  190 (192)
                      +++|++.|+|+||||.++|++|+.+. ..+|+++++++....
T Consensus       185 ~~~i~~~c~glPLal~~~a~~l~~~~~~~~w~~~~~~l~~~~  226 (287)
T PF00931_consen  185 AKEIVEKCGGLPLALKLIASYLRSKSTVDEWEEALEELENSL  226 (287)
T ss_dssp             HHHHHHHTTT-HHHHHHHHHHHHHHHSSSSHHHHHHHHHHCH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccc
Confidence            89999999999999999999997654 889999998887543

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.

>PLN03210 Resistant to P

Probab=99.97  E-value=1.3e-28  Score=218.75  Aligned_cols=190  Identities=36%  Similarity=0.586  Sum_probs=155.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeec--ccc---ccC-----CCChHHHHHHHHHHHhcCCCC-cCchHHHHhhcCCce
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENV--REE---SQR-----PGGLACLRQKLLSNILKDKNV-MPYIDLNFRRLSRMK   69 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~--~~~---~~~-----~~~~~~~~~~l~~~~~~~~~~-~~~~~~l~~~l~~~~   69 (192)
                      +||||||+.+|+++..+|++.+|+...  +..   ...     ......+...++..+...... ......+++.+.+++
T Consensus       218 iGKTTLA~~l~~~l~~~F~g~vfv~~~~v~~~~~~~~~~~~~~~~~~~~l~~~~l~~il~~~~~~~~~~~~~~~~L~~kr  297 (1153)
T PLN03210        218 IGKTTIARALFSRLSRQFQSSVFIDRAFISKSMEIYSSANPDDYNMKLHLQRAFLSEILDKKDIKIYHLGAMEERLKHRK  297 (1153)
T ss_pred             CchHHHHHHHHHHHhhcCCeEEEeeccccccchhhcccccccccchhHHHHHHHHHHHhCCCCcccCCHHHHHHHHhCCe
Confidence            799999999999999999999888531  110   000     001233455556665544332 334467888899999


Q ss_pred             EEEEEeCCCCchhHHHhhccCCCCCCCceEEEEecchhHHhhcCCCceEecCCCCHHHHHHHHHHhhcCCCCCCccHHHH
Q 039644           70 VLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKL  149 (192)
Q Consensus        70 ~LlVlDdv~~~~~~~~l~~~~~~~~~~~~iivTtR~~~~~~~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~  149 (192)
                      +||||||||+..+|+.+.....+.++|++||||||++.++...+..+.++++.++.++|++||.++||....+++.+.++
T Consensus       298 vLLVLDdv~~~~~l~~L~~~~~~~~~GsrIIiTTrd~~vl~~~~~~~~~~v~~l~~~ea~~LF~~~Af~~~~~~~~~~~l  377 (1153)
T PLN03210        298 VLIFIDDLDDQDVLDALAGQTQWFGSGSRIIVITKDKHFLRAHGIDHIYEVCLPSNELALEMFCRSAFKKNSPPDGFMEL  377 (1153)
T ss_pred             EEEEEeCCCCHHHHHHHHhhCccCCCCcEEEEEeCcHHHHHhcCCCeEEEecCCCHHHHHHHHHHHhcCCCCCcHHHHHH
Confidence            99999999999999999876666788999999999999988777778999999999999999999999876666778899


Q ss_pred             HHHHHHHhCCCchHHHHHHHHhccCCHHHHHHHHHHHHhcC
Q 039644          150 SSNVTKYAQGIPLALKVLSCFLHKREKEVWESAIDKLQRIL  190 (192)
Q Consensus       150 ~~~i~~~~~g~Plai~~~~~~l~~~~~~~w~~~l~~l~~~~  190 (192)
                      +.+|++.|+|+|||++++|++|++++..+|+.++++++..+
T Consensus       378 ~~~iv~~c~GLPLAl~vlgs~L~~k~~~~W~~~l~~L~~~~  418 (1153)
T PLN03210        378 ASEVALRAGNLPLGLNVLGSYLRGRDKEDWMDMLPRLRNGL  418 (1153)
T ss_pred             HHHHHHHhCCCcHHHHHHHHHHcCCCHHHHHHHHHHHHhCc
Confidence            99999999999999999999999988999999999998754

syringae 6; Provisional

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

Probab=99.05  E-value=8.3e-08  Score=73.30  Aligned_cols=180  Identities=14%  Similarity=0.158  Sum_probs=106.4

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcC---chHHHH----hhc-CCceEEE
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMP---YIDLNF----RRL-SRMKVLI   72 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~---~~~~l~----~~l-~~~~~Ll   72 (192)
                      +|||||++.++..+...=...+|+. ...     .+..+++..+...++.......   ....+.    ... .+++.++
T Consensus        54 ~GKTtl~~~l~~~l~~~~~~~~~~~-~~~-----~~~~~~l~~i~~~lG~~~~~~~~~~~~~~l~~~l~~~~~~~~~~vl  127 (269)
T TIGR03015        54 AGKTTLIRNLLKRLDQERVVAAKLV-NTR-----VDAEDLLRMVAADFGLETEGRDKAALLRELEDFLIEQFAAGKRALL  127 (269)
T ss_pred             CCHHHHHHHHHHhcCCCCeEEeeee-CCC-----CCHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHHHHhCCCCeEE
Confidence            6999999999998653211223332 111     4667888888877754332211   222222    222 5678999


Q ss_pred             EEeCCCCch--hHHHhhc---cCCCCCCCceEEEEecchhHHhhc----------CCCceEecCCCCHHHHHHHHHHhhc
Q 039644           73 VFDDVTCFS--QLESLMG---SLDWLTPVSRIILTTRNKQVLRNW----------GVSKIYEMEALEYHHALELFSQHAF  137 (192)
Q Consensus        73 VlDdv~~~~--~~~~l~~---~~~~~~~~~~iivTtR~~~~~~~~----------~~~~~~~l~~l~~~ea~~lf~~~~~  137 (192)
                      |+|+++...  .++.+..   ..........|++|.... .....          .....+.+++++.+|..+++.....
T Consensus       128 iiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~~~-~~~~l~~~~~~~l~~r~~~~~~l~~l~~~e~~~~l~~~l~  206 (269)
T TIGR03015       128 VVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPE-FRETLQSPQLQQLRQRIIASCHLGPLDREETREYIEHRLE  206 (269)
T ss_pred             EEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCCHH-HHHHHcCchhHHHHhheeeeeeCCCCCHHHHHHHHHHHHH
Confidence            999998754  3444332   111112233455554332 21111          1134678999999999998887654


Q ss_pred             CCC--CCCccHHHHHHHHHHHhCCCchHHHHHHHHhc------cCC---HHHHHHHHHHHH
Q 039644          138 KRN--HPDVGYEKLSSNVTKYAQGIPLALKVLSCFLH------KRE---KEVWESAIDKLQ  187 (192)
Q Consensus       138 ~~~--~~~~~~~~~~~~i~~~~~g~Plai~~~~~~l~------~~~---~~~w~~~l~~l~  187 (192)
                      ...  ....-..+..+.|.+.++|.|..|..++..+-      +..   .+.++.++.++.
T Consensus       207 ~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~  267 (269)
T TIGR03015       207 RAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEID  267 (269)
T ss_pred             HcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhh
Confidence            322  11234557888999999999999999887661      221   566666665543

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.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.97  E-value=1.8e-08  Score=88.96  Aligned_cols=160  Identities=16%  Similarity=0.158  Sum_probs=99.0

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-----c--------C----chHHHHh
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV-----M--------P----YIDLNFR   63 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-----~--------~----~~~~l~~   63 (192)
                      .||||++.++....    +.++|++ +.+.+   .+...+...++..+....+.     .        .    ....+..
T Consensus        43 ~GKTtl~~~~~~~~----~~~~w~~-l~~~d---~~~~~f~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  114 (903)
T PRK04841         43 YGKTTLISQWAAGK----NNLGWYS-LDESD---NQPERFASYLIAALQQATNGHCSKSEALAQKRQYASLSSLFAQLFI  114 (903)
T ss_pred             CCHHHHHHHHHHhC----CCeEEEe-cCccc---CCHHHHHHHHHHHHHHhcCcccchhhhhhccCCcCCHHHHHHHHHH
Confidence            49999999988643    3689997 43322   34556666666666421110     0        0    2223333


Q ss_pred             hcC--CceEEEEEeCCCCchh--H-HHhhccCCCCCCCceEEEEecchhHHhhc---CCCceEecC----CCCHHHHHHH
Q 039644           64 RLS--RMKVLIVFDDVTCFSQ--L-ESLMGSLDWLTPVSRIILTTRNKQVLRNW---GVSKIYEME----ALEYHHALEL  131 (192)
Q Consensus        64 ~l~--~~~~LlVlDdv~~~~~--~-~~l~~~~~~~~~~~~iivTtR~~~~~~~~---~~~~~~~l~----~l~~~ea~~l  131 (192)
                      .+.  +.+.+|||||+.....  . +.+..-++...++.++|||||........   -......+.    +|+.+|+.++
T Consensus       115 ~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~~~~~~~~~l~~~~~~~~l~~~~l~f~~~e~~~l  194 (903)
T PRK04841        115 ELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRNLPPLGIANLRVRDQLLEIGSQQLAFDHQEAQQF  194 (903)
T ss_pred             HHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCCCCCCchHhHHhcCcceecCHHhCCCCHHHHHHH
Confidence            332  6799999999986431  2 22222233334567899999984322111   112344555    8999999999


Q ss_pred             HHHhhcCCCCCCccHHHHHHHHHHHhCCCchHHHHHHHHhcc
Q 039644          132 FSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHK  173 (192)
Q Consensus       132 f~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plai~~~~~~l~~  173 (192)
                      |....+..     -..+.+..+.+.|+|+|+++..++..++.
T Consensus       195 l~~~~~~~-----~~~~~~~~l~~~t~Gwp~~l~l~~~~~~~  231 (903)
T PRK04841        195 FDQRLSSP-----IEAAESSRLCDDVEGWATALQLIALSARQ  231 (903)
T ss_pred             HHhccCCC-----CCHHHHHHHHHHhCChHHHHHHHHHHHhh
Confidence            97765322     13455678999999999999998876643

>PF05729 NACHT: NACHT domain

Probab=98.95  E-value=1.4e-08  Score=71.60  Aligned_cols=132  Identities=20%  Similarity=0.328  Sum_probs=77.1

Q ss_pred             CchhHHHHHHHHHhhCC------CcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhc-CCceEEEE
Q 039644            1 IGKTAIARAIFDKISGD------FECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRL-SRMKVLIV   73 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~------F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l-~~~~~LlV   73 (192)
                      +||||++..++.+....      +...+|+. .+..... .....+...+..+.......  ....+...+ ...+++||
T Consensus        11 ~GKStll~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~-~~~~~l~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~lli   86 (166)
T PF05729_consen   11 SGKSTLLRKLAQQLAEEEPPPSKFPYPFFFS-LRDISDS-NNSRSLADLLFDQLPESIAP--IEELLQELLEKNKRVLLI   86 (166)
T ss_pred             CChHHHHHHHHHHHHhcCcccccceEEEEEe-ehhhhhc-cccchHHHHHHHhhccchhh--hHHHHHHHHHcCCceEEE
Confidence            69999999999965433      23455554 4332222 11123333333333322221  111122222 56899999


Q ss_pred             EeCCCCchh---------HHHhh-ccCCC-CCCCceEEEEecchhHH---hhcCCCceEecCCCCHHHHHHHHHHhh
Q 039644           74 FDDVTCFSQ---------LESLM-GSLDW-LTPVSRIILTTRNKQVL---RNWGVSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus        74 lDdv~~~~~---------~~~l~-~~~~~-~~~~~~iivTtR~~~~~---~~~~~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      ||++++...         +..+. ..++. ..+++++++|||.....   ........+.+.+++.++..+++.++.
T Consensus        87 lDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~f  163 (166)
T PF05729_consen   87 LDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFPDLRRRLKQAQILELEPFSEEDIKQYLRKYF  163 (166)
T ss_pred             EechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHHHHHHhcCCCcEEEECCCCHHHHHHHHHHHh
Confidence            999986532         22222 22222 24688999999987662   223444679999999999999987764

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

Probab=98.77  E-value=9.8e-08  Score=70.94  Aligned_cols=162  Identities=17%  Similarity=0.228  Sum_probs=79.5

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHH------HHHHHHHHh----cCC---------CC-cCchHH
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACL------RQKLLSNIL----KDK---------NV-MPYIDL   60 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~------~~~l~~~~~----~~~---------~~-~~~~~~   60 (192)
                      +|||+|++++.+..++.-...+|+.........  ....+      ...+...+.    ...         .. ......
T Consensus        31 ~GKTsLl~~~~~~~~~~~~~~~y~~~~~~~~~~--~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  108 (234)
T PF01637_consen   31 SGKTSLLKEFINELKEKGYKVVYIDFLEESNES--SLRSFIEETSLADELSEALGISIPSITLEKISKDLSEDSFSALER  108 (234)
T ss_dssp             SSHHHHHHHHHHHCT--EECCCHHCCTTBSHHH--HHHHHHHHHHHHCHCHHHHHHHCCTSTTEEEECTS-GG-G--HHH
T ss_pred             CCHHHHHHHHHHHhhhcCCcEEEEecccchhhh--HHHHHHHHHHHHHHHHHHHhhhcccccchhhhhcchhhHHHHHHH
Confidence            699999999999875443345555432221100  11111      011111121    100         01 114444


Q ss_pred             HHhhcC--CceEEEEEeCCCCch----h-------HHHhhccCCCCCCCceEEEEecchhHHhh--------cCCCceEe
Q 039644           61 NFRRLS--RMKVLIVFDDVTCFS----Q-------LESLMGSLDWLTPVSRIILTTRNKQVLRN--------WGVSKIYE  119 (192)
Q Consensus        61 l~~~l~--~~~~LlVlDdv~~~~----~-------~~~l~~~~~~~~~~~~iivTtR~~~~~~~--------~~~~~~~~  119 (192)
                      +...+.  +++.+||+|+++...    .       +..+........+. .+|++.........        .+....+.
T Consensus       109 ~~~~l~~~~~~~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~-~~v~~~S~~~~~~~~~~~~~~~~~~~~~~~  187 (234)
T PF01637_consen  109 LLEKLKKKGKKVIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQNV-SIVITGSSDSLMEEFLDDKSPLFGRFSHIE  187 (234)
T ss_dssp             HHHHHHHCHCCEEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----TTE-EEEEEESSHHHHHHTT-TTSTTTT---EEE
T ss_pred             HHHHHHhcCCcEEEEEecHHHHhhcccchHHHHHHHHHHHhhccccCCc-eEEEECCchHHHHHhhcccCccccccceEE
Confidence            444443  345999999997655    1       22333333323333 45555554444433        13344599


Q ss_pred             cCCCCHHHHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCCchHHHH
Q 039644          120 MEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKV  166 (192)
Q Consensus       120 l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plai~~  166 (192)
                      +++++.+++.+++.........- +......++|...+||+|..|..
T Consensus       188 l~~l~~~e~~~~~~~~~~~~~~~-~~~~~~~~~i~~~~gG~P~~l~~  233 (234)
T PF01637_consen  188 LKPLSKEEAREFLKELFKELIKL-PFSDEDIEEIYSLTGGNPRYLQE  233 (234)
T ss_dssp             E----HHHHHHHHHHHHHCC-------HHHHHHHHHHHTT-HHHHHH
T ss_pred             EeeCCHHHHHHHHHHHHHHhhcc-cCCHHHHHHHHHHhCCCHHHHhc
Confidence            99999999999999865433111 22456678999999999998764

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

>PF13173 AAA_14: AAA domain

Probab=98.64  E-value=2.9e-07  Score=62.54  Aligned_cols=109  Identities=17%  Similarity=0.184  Sum_probs=69.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||||+++++++.. .-..+++++....         ........+         ..+.+.+....+..+++||++...
T Consensus        13 vGKTtll~~~~~~~~-~~~~~~yi~~~~~---------~~~~~~~~~---------~~~~~~~~~~~~~~~i~iDEiq~~   73 (128)
T PF13173_consen   13 VGKTTLLKQLAKDLL-PPENILYINFDDP---------RDRRLADPD---------LLEYFLELIKPGKKYIFIDEIQYL   73 (128)
T ss_pred             CCHHHHHHHHHHHhc-ccccceeeccCCH---------HHHHHhhhh---------hHHHHHHhhccCCcEEEEehhhhh
Confidence            799999999998765 3345666652211         111000000         112233333346788999999988


Q ss_pred             hhHHHhhccCCCCCCCceEEEEecchhHHhhc------CCCceEecCCCCHHHH
Q 039644           81 SQLESLMGSLDWLTPVSRIILTTRNKQVLRNW------GVSKIYEMEALEYHHA  128 (192)
Q Consensus        81 ~~~~~l~~~~~~~~~~~~iivTtR~~~~~~~~------~~~~~~~l~~l~~~ea  128 (192)
                      .+|......+-+...+.+|++|+.........      +....++|.||+..|.
T Consensus        74 ~~~~~~lk~l~d~~~~~~ii~tgS~~~~l~~~~~~~l~gr~~~~~l~Plsf~E~  127 (128)
T PF13173_consen   74 PDWEDALKFLVDNGPNIKIILTGSSSSLLSKDIAESLAGRVIEIELYPLSFREF  127 (128)
T ss_pred             ccHHHHHHHHHHhccCceEEEEccchHHHhhcccccCCCeEEEEEECCCCHHHh
Confidence            88877766666555678999999876665332      3445688999988763

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.54  E-value=6.6e-06  Score=66.32  Aligned_cols=181  Identities=11%  Similarity=0.113  Sum_probs=99.8

Q ss_pred             CchhHHHHHHHHHhhCCCc--ceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC---cC---chHHHHhhcC--CceE
Q 039644            1 IGKTAIARAIFDKISGDFE--CSCFLENVREESQRPGGLACLRQKLLSNILKDKNV---MP---YIDLNFRRLS--RMKV   70 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~--~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---~~---~~~~l~~~l~--~~~~   70 (192)
                      +|||++++.+++++.....  ..+++.....     .+...++..++.++......   ..   ....+...+.  +++.
T Consensus        66 tGKT~l~~~v~~~l~~~~~~~~~v~in~~~~-----~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  140 (394)
T PRK00411         66 TGKTTTVKKVFEELEEIAVKVVYVYINCQID-----RTRYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVL  140 (394)
T ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEEEECCcC-----CCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEE
Confidence            6999999999998765542  2344442211     45678888888888652211   11   4455555554  4578


Q ss_pred             EEEEeCCCCch------hHHHhhccCCCCC-CCceEEEEecchhHHhhcC-------CCceEecCCCCHHHHHHHHHHhh
Q 039644           71 LIVFDDVTCFS------QLESLMGSLDWLT-PVSRIILTTRNKQVLRNWG-------VSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus        71 LlVlDdv~~~~------~~~~l~~~~~~~~-~~~~iivTtR~~~~~~~~~-------~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      +||||+++...      .+..+........ ....+|.++..........       ....+.+++++.++..+++..++
T Consensus       141 viviDE~d~l~~~~~~~~l~~l~~~~~~~~~~~v~vI~i~~~~~~~~~l~~~~~s~~~~~~i~f~py~~~e~~~il~~r~  220 (394)
T PRK00411        141 IVALDDINYLFEKEGNDVLYSLLRAHEEYPGARIGVIGISSDLTFLYILDPRVKSVFRPEEIYFPPYTADEIFDILKDRV  220 (394)
T ss_pred             EEEECCHhHhhccCCchHHHHHHHhhhccCCCeEEEEEEECCcchhhhcCHHHHhcCCcceeecCCCCHHHHHHHHHHHH
Confidence            99999998642      2444433222211 1223556655543322211       13467899999999999988776


Q ss_pred             cCCCCCCccHHHHHHHHHHH----hCCCchHHHHHHHHh-----ccC---CHHHHHHHHHHH
Q 039644          137 FKRNHPDVGYEKLSSNVTKY----AQGIPLALKVLSCFL-----HKR---EKEVWESAIDKL  186 (192)
Q Consensus       137 ~~~~~~~~~~~~~~~~i~~~----~~g~Plai~~~~~~l-----~~~---~~~~w~~~l~~l  186 (192)
                      .....+..-.++..+.+.+.    .|..+.|+.++-...     ++.   +.+..+++++++
T Consensus       221 ~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~  282 (394)
T PRK00411        221 EEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKS  282 (394)
T ss_pred             HhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence            32211111122233333333    455677776654322     111   255565665554

>PRK06893 DNA replication initiation factor; Validated

Probab=98.53  E-value=2.2e-06  Score=64.06  Aligned_cols=141  Identities=11%  Similarity=0.183  Sum_probs=82.8

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||+|+..+++....+.....|+.. ..       .......+                 ...+. ..-+|+|||++..
T Consensus        50 ~GKThL~~ai~~~~~~~~~~~~y~~~-~~-------~~~~~~~~-----------------~~~~~-~~dlLilDDi~~~  103 (229)
T PRK06893         50 SGKSHLLKAVSNHYLLNQRTAIYIPL-SK-------SQYFSPAV-----------------LENLE-QQDLVCLDDLQAV  103 (229)
T ss_pred             CCHHHHHHHHHHHHHHcCCCeEEeeH-HH-------hhhhhHHH-----------------Hhhcc-cCCEEEEeChhhh
Confidence            69999999999987655556677762 11       01111111                 11111 2248999999863


Q ss_pred             ---hhHH-HhhccCCCC-CCCceEEE-Eecc---------hhHHhhcCCCceEecCCCCHHHHHHHHHHhhcCCCCCCcc
Q 039644           81 ---SQLE-SLMGSLDWL-TPVSRIIL-TTRN---------KQVLRNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVG  145 (192)
Q Consensus        81 ---~~~~-~l~~~~~~~-~~~~~iiv-TtR~---------~~~~~~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~  145 (192)
                         ..|+ .+...+... ..+..+|+ |++.         +.+...+.....+.+++++.++.++++.+.+....  -.-
T Consensus       104 ~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~~~iL~~~a~~~~--l~l  181 (229)
T PRK06893        104 IGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQLNDLTDEQKIIVLQRNAYQRG--IEL  181 (229)
T ss_pred             cCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHHHHhcCCeeeCCCCCHHHHHHHHHHHHHHcC--CCC
Confidence               3344 222222211 23555655 4443         34555555567899999999999999998875432  222


Q ss_pred             HHHHHHHHHHHhCCCchHHHHHHH
Q 039644          146 YEKLSSNVTKYAQGIPLALKVLSC  169 (192)
Q Consensus       146 ~~~~~~~i~~~~~g~Plai~~~~~  169 (192)
                      .++...-|++.+.|..-++..+-.
T Consensus       182 ~~~v~~~L~~~~~~d~r~l~~~l~  205 (229)
T PRK06893        182 SDEVANFLLKRLDRDMHTLFDALD  205 (229)
T ss_pred             CHHHHHHHHHhccCCHHHHHHHHH
Confidence            345566677778777665544443

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

Probab=98.44  E-value=3e-06  Score=66.85  Aligned_cols=138  Identities=20%  Similarity=0.264  Sum_probs=85.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCC-
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTC-   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~-   79 (192)
                      +||||||+.++......|...-=+.         .++.++..-+.+.             -.....+++.+|.+|.++. 
T Consensus        59 ~GKTTlA~liA~~~~~~f~~~sAv~---------~gvkdlr~i~e~a-------------~~~~~~gr~tiLflDEIHRf  116 (436)
T COG2256          59 TGKTTLARLIAGTTNAAFEALSAVT---------SGVKDLREIIEEA-------------RKNRLLGRRTILFLDEIHRF  116 (436)
T ss_pred             CCHHHHHHHHHHhhCCceEEecccc---------ccHHHHHHHHHHH-------------HHHHhcCCceEEEEehhhhc
Confidence            6999999999998887776533332         3444544322111             1222347899999999974 


Q ss_pred             -chhHHHhhccCCCCCCCceEEE--EecchhHHhhc---CCCceEecCCCCHHHHHHHHHHhhcCCCC-----CCccHHH
Q 039644           80 -FSQLESLMGSLDWLTPVSRIIL--TTRNKQVLRNW---GVSKIYEMEALEYHHALELFSQHAFKRNH-----PDVGYEK  148 (192)
Q Consensus        80 -~~~~~~l~~~~~~~~~~~~iiv--TtR~~~~~~~~---~~~~~~~l~~l~~~ea~~lf~~~~~~~~~-----~~~~~~~  148 (192)
                       ..+-+.|.   |....|.-++|  ||.++...-..   +...++.+++|+.++...++.+.......     .....++
T Consensus       117 nK~QQD~lL---p~vE~G~iilIGATTENPsF~ln~ALlSR~~vf~lk~L~~~di~~~l~ra~~~~~rgl~~~~~~i~~~  193 (436)
T COG2256         117 NKAQQDALL---PHVENGTIILIGATTENPSFELNPALLSRARVFELKPLSSEDIKKLLKRALLDEERGLGGQIIVLDEE  193 (436)
T ss_pred             Chhhhhhhh---hhhcCCeEEEEeccCCCCCeeecHHHhhhhheeeeecCCHHHHHHHHHHHHhhhhcCCCcccccCCHH
Confidence             34456654   44456776776  66665533222   56789999999999999999884321111     1112334


Q ss_pred             HHHHHHHHhCCCchH
Q 039644          149 LSSNVTKYAQGIPLA  163 (192)
Q Consensus       149 ~~~~i~~~~~g~Pla  163 (192)
                      ...-++..++|--.+
T Consensus       194 a~~~l~~~s~GD~R~  208 (436)
T COG2256         194 ALDYLVRLSNGDARR  208 (436)
T ss_pred             HHHHHHHhcCchHHH
Confidence            555666666666443

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=98.37  E-value=1e-05  Score=69.29  Aligned_cols=160  Identities=14%  Similarity=0.154  Sum_probs=106.7

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC--cC---------------chHHHHh
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV--MP---------------YIDLNFR   63 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--~~---------------~~~~l~~   63 (192)
                      -|||||+-+.+.... .=..+.|++.....    -+...+.+.++..+...-+.  .+               +.+.+..
T Consensus        48 fGKttl~aq~~~~~~-~~~~v~Wlslde~d----ndp~rF~~yLi~al~~~~p~~~~~a~~l~q~~~~~~l~~l~~~L~~  122 (894)
T COG2909          48 FGKTTLLAQWRELAA-DGAAVAWLSLDESD----NDPARFLSYLIAALQQATPTLGDEAQTLLQKHQYVSLESLLSSLLN  122 (894)
T ss_pred             CcHHHHHHHHHHhcC-cccceeEeecCCcc----CCHHHHHHHHHHHHHHhCccccHHHHHHHHhcccccHHHHHHHHHH
Confidence            399999999998433 34688999843221    47788888888877643332  11               4444555


Q ss_pred             hcC--CceEEEEEeCCCCchh------HHHhhccCCCCCCCceEEEEecchhHHhhcC---CCceEecC----CCCHHHH
Q 039644           64 RLS--RMKVLIVFDDVTCFSQ------LESLMGSLDWLTPVSRIILTTRNKQVLRNWG---VSKIYEME----ALEYHHA  128 (192)
Q Consensus        64 ~l~--~~~~LlVlDdv~~~~~------~~~l~~~~~~~~~~~~iivTtR~~~~~~~~~---~~~~~~l~----~l~~~ea  128 (192)
                      .+.  .++..+||||..-..+      ++.+....   ..+-.+|+|||.........   ....++++    .++.+|+
T Consensus       123 Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~---P~~l~lvv~SR~rP~l~la~lRlr~~llEi~~~~Lrf~~eE~  199 (894)
T COG2909         123 ELASYEGPLYLVLDDYHLISDPALHEALRFLLKHA---PENLTLVVTSRSRPQLGLARLRLRDELLEIGSEELRFDTEEA  199 (894)
T ss_pred             HHHhhcCceEEEeccccccCcccHHHHHHHHHHhC---CCCeEEEEEeccCCCCcccceeehhhHHhcChHhhcCChHHH
Confidence            443  3689999999975432      45554443   45778999999865433321   11222333    4889999


Q ss_pred             HHHHHHhhcCCCCCCccHHHHHHHHHHHhCCCchHHHHHHHHhcc
Q 039644          129 LELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHK  173 (192)
Q Consensus       129 ~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plai~~~~~~l~~  173 (192)
                      .++|....+.     +......+.+++..+|.+-|+..++=.++.
T Consensus       200 ~~fl~~~~~l-----~Ld~~~~~~L~~~teGW~~al~L~aLa~~~  239 (894)
T COG2909         200 AAFLNDRGSL-----PLDAADLKALYDRTEGWAAALQLIALALRN  239 (894)
T ss_pred             HHHHHHcCCC-----CCChHHHHHHHhhcccHHHHHHHHHHHccC
Confidence            9988776422     223455778999999999999999988883

>COG3903 Predicted ATPase [General function prediction only]

Probab=98.30  E-value=9.4e-07  Score=69.82  Aligned_cols=167  Identities=17%  Similarity=0.196  Sum_probs=111.8

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-cCchHHHHhhcCCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV-MPYIDLNFRRLSRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~~~~~l~~~l~~~~~LlVlDdv~~   79 (192)
                      |||||++-.+.. +..-|....|+....++    .+...+.-.+...+.-.... ......+..+..+++.++|+||...
T Consensus        25 vgkttl~~~~a~-~~~~~~~~v~~vdl~pi----tD~~~v~~~~ag~~gl~~~~g~~~~~~~~~~~~~rr~llvldnceh   99 (414)
T COG3903          25 VGKTTLALQAAH-AASEYADGVAFVDLAPI----TDPALVFPTLAGALGLHVQPGDSAVDTLVRRIGDRRALLVLDNCEH   99 (414)
T ss_pred             cceehhhhhhHh-Hhhhcccceeeeecccc----CchhHhHHHHHhhcccccccchHHHHHHHHHHhhhhHHHHhcCcHH
Confidence            799999999999 88889877777656664    33444444443333322221 2255567778889999999999975


Q ss_pred             chh-HHHhhccCCCCCCCceEEEEecchhHHhhcCCCceEecCCCCHH-HHHHHHHHhhcCCCC---CCccHHHHHHHHH
Q 039644           80 FSQ-LESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEMEALEYH-HALELFSQHAFKRNH---PDVGYEKLSSNVT  154 (192)
Q Consensus        80 ~~~-~~~l~~~~~~~~~~~~iivTtR~~~~~~~~~~~~~~~l~~l~~~-ea~~lf~~~~~~~~~---~~~~~~~~~~~i~  154 (192)
                      ..+ -..+...+..+++.-.++.|+|.....   .+...+.+++++.. ++.++|...+.....   -.......+.+|+
T Consensus       100 l~~~~a~~i~all~~~~~~~~~atsre~~l~---~ge~~~~~~~L~~~d~a~~lf~~ra~~~~~~f~l~~~~~a~v~~ic  176 (414)
T COG3903         100 LLDACAALIVALLGACPRLAILATSREAILV---AGEVHRRVPSLSLFDEAIELFVCRAVLVALSFWLTDDNAAAVAEIC  176 (414)
T ss_pred             HHHHHHHHHHHHHccchhhhhHHHhHhhhcc---cccccccCCccccCCchhHHHHHHHHHhccceeecCCchHHHHHHH
Confidence            533 222222333345556688888865432   34556777777765 788998877643221   1234466788999


Q ss_pred             HHhCCCchHHHHHHHHhccCC
Q 039644          155 KYAQGIPLALKVLSCFLHKRE  175 (192)
Q Consensus       155 ~~~~g~Plai~~~~~~l~~~~  175 (192)
                      +..+|.|++|..+++..+.-.
T Consensus       177 r~ldg~~laielaaarv~sl~  197 (414)
T COG3903         177 RRLDGIPLAIELAAARVRSLS  197 (414)
T ss_pred             HHhhcchHHHHHHHHHHHhcC
Confidence            999999999999999887754

>PF14516 AAA_35: AAA-like domain

Probab=98.28  E-value=5.6e-05  Score=59.66  Aligned_cols=166  Identities=11%  Similarity=0.228  Sum_probs=94.8

Q ss_pred             CchhHHHHHHHHHhh-CCCcceEEEeecccccc-CCCChHHHHHHHHHHHhcCCCC---------------cCchHHHHh
Q 039644            1 IGKTAIARAIFDKIS-GDFECSCFLENVREESQ-RPGGLACLRQKLLSNILKDKNV---------------MPYIDLNFR   63 (192)
Q Consensus         1 iGKTtLa~~~~~~~~-~~F~~~~wv~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~---------------~~~~~~l~~   63 (192)
                      +|||+|...+.+..+ +.|.+ ++++ ...... ...+...+++.++..+...-..               ......+.+
T Consensus        42 ~GKTSll~~l~~~l~~~~~~~-v~id-~~~~~~~~~~~~~~f~~~~~~~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~  119 (331)
T PF14516_consen   42 MGKTSLLLRLLERLQQQGYRC-VYID-LQQLGSAIFSDLEQFLRWFCEEISRQLKLDEKLDEYWDEEIGSKISCTEYFEE  119 (331)
T ss_pred             CCHHHHHHHHHHHHHHCCCEE-EEEE-eecCCCcccCCHHHHHHHHHHHHHHHcCCChhHHHHHHHhcCChhhHHHHHHH
Confidence            699999999999875 44444 5665 322211 2235666666666555432111               113333443


Q ss_pred             hc---CCceEEEEEeCCCCchh--------HHHhhccCCCC--C--CC-ceEEEEecchh-HHh-----hcCCCceEecC
Q 039644           64 RL---SRMKVLIVFDDVTCFSQ--------LESLMGSLDWL--T--PV-SRIILTTRNKQ-VLR-----NWGVSKIYEME  121 (192)
Q Consensus        64 ~l---~~~~~LlVlDdv~~~~~--------~~~l~~~~~~~--~--~~-~~iivTtR~~~-~~~-----~~~~~~~~~l~  121 (192)
                      .+   .+++.+|+||+++....        +..++......  .  .. -++++....+. ...     ++.....+.|+
T Consensus       120 ~ll~~~~~~lVL~iDEiD~l~~~~~~~~dF~~~LR~~~~~~~~~~~~~~L~li~~~~t~~~~~~~~~~SPFNIg~~i~L~  199 (331)
T PF14516_consen  120 YLLKQIDKPLVLFIDEIDRLFEYPQIADDFFGLLRSWYEQRKNNPIWQKLRLILAGSTEDYIILDINQSPFNIGQPIELP  199 (331)
T ss_pred             HHHhcCCCCEEEEEechhhhccCcchHHHHHHHHHHHHHhcccCcccceEEEEEecCcccccccCCCCCCcccccceeCC
Confidence            32   26899999999985421        22222111110  0  11 11222211111 111     11235678899


Q ss_pred             CCCHHHHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCCchHHHHHHHHhccC
Q 039644          122 ALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKR  174 (192)
Q Consensus       122 ~l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plai~~~~~~l~~~  174 (192)
                      +++.+|...|...+...      .-....+.+...++|||.-+..++..|...
T Consensus       200 ~Ft~~ev~~L~~~~~~~------~~~~~~~~l~~~tgGhP~Lv~~~~~~l~~~  246 (331)
T PF14516_consen  200 DFTPEEVQELAQRYGLE------FSQEQLEQLMDWTGGHPYLVQKACYLLVEE  246 (331)
T ss_pred             CCCHHHHHHHHHhhhcc------CCHHHHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence            99999999998876422      112237889999999999999999988664

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=98.21  E-value=0.00011  Score=53.24  Aligned_cols=89  Identities=17%  Similarity=0.233  Sum_probs=61.6

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +.+-++|+|+++...  ..+.+...+.+....+.+|++|++.. +.... +....+.+.+++.++..+.+...  + .  
T Consensus        95 ~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~i~sr~~~~~~~~~~~~~~~~~l~~~--g-i--  169 (188)
T TIGR00678        95 SGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSPEKLLPTIRSRCQVLPFPPLSEEALLQWLIRQ--G-I--  169 (188)
T ss_pred             CCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhChHHHHhhcEEeeCCCCCHHHHHHHHHHc--C-C--
Confidence            456689999998653  36667666665555677777776542 11111 34578999999999998888776  1 1  


Q ss_pred             CccHHHHHHHHHHHhCCCchH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Pla  163 (192)
                         ..+.+..+++.++|.|..
T Consensus       170 ---~~~~~~~i~~~~~g~~r~  187 (188)
T TIGR00678       170 ---SEEAAELLLALAGGSPGA  187 (188)
T ss_pred             ---CHHHHHHHHHHcCCCccc
Confidence               245677899999998863

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.

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.21  E-value=0.00022  Score=56.92  Aligned_cols=159  Identities=14%  Similarity=0.159  Sum_probs=89.2

Q ss_pred             CchhHHHHHHHHHhhCCCc------ceEEEeeccccccCCCChHHHHHHHHHHHhc---CCCC--cC---chHHHHhhcC
Q 039644            1 IGKTAIARAIFDKISGDFE------CSCFLENVREESQRPGGLACLRQKLLSNILK---DKNV--MP---YIDLNFRRLS   66 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~------~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~---~~~~--~~---~~~~l~~~l~   66 (192)
                      +|||++++.+++.+.+...      ..+|+.....     .+...++..++.++..   ..+.  ..   ....+...+.
T Consensus        51 tGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~-----~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~  125 (365)
T TIGR02928        51 TGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQIL-----DTLYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELN  125 (365)
T ss_pred             CCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCC-----CCHHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHH
Confidence            6999999999997643322      2345542211     4567888888888842   1111  11   3344555553


Q ss_pred             --CceEEEEEeCCCCch-----hHHHhhcc--CCCCC-CCceEEEEecchhHHhhc------C-CCceEecCCCCHHHHH
Q 039644           67 --RMKVLIVFDDVTCFS-----QLESLMGS--LDWLT-PVSRIILTTRNKQVLRNW------G-VSKIYEMEALEYHHAL  129 (192)
Q Consensus        67 --~~~~LlVlDdv~~~~-----~~~~l~~~--~~~~~-~~~~iivTtR~~~~~~~~------~-~~~~~~l~~l~~~ea~  129 (192)
                        +++++||||+++...     .+..+...  ..... ....+|.+++........      . ....+.+++.+.++..
T Consensus       126 ~~~~~~vlvIDE~d~L~~~~~~~L~~l~~~~~~~~~~~~~v~lI~i~n~~~~~~~l~~~~~s~~~~~~i~f~p~~~~e~~  205 (365)
T TIGR02928       126 ERGDSLIIVLDEIDYLVGDDDDLLYQLSRARSNGDLDNAKVGVIGISNDLKFRENLDPRVKSSLCEEEIIFPPYDAEELR  205 (365)
T ss_pred             hcCCeEEEEECchhhhccCCcHHHHhHhccccccCCCCCeEEEEEEECCcchHhhcCHHHhccCCcceeeeCCCCHHHHH
Confidence              568899999998651     13333322  11111 233455555544322111      1 1256889999999999


Q ss_pred             HHHHHhhcCC---CCCCccHHHHHHHHHHHhCCCchHH
Q 039644          130 ELFSQHAFKR---NHPDVGYEKLSSNVTKYAQGIPLAL  164 (192)
Q Consensus       130 ~lf~~~~~~~---~~~~~~~~~~~~~i~~~~~g~Plai  164 (192)
                      +++..++...   ..-++...++...++....|.|..+
T Consensus       206 ~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~a  243 (365)
T TIGR02928       206 DILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKA  243 (365)
T ss_pred             HHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHH
Confidence            9998876311   1112333334555666677887543

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.

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=98.20  E-value=4.4e-05  Score=62.62  Aligned_cols=153  Identities=13%  Similarity=0.199  Sum_probs=91.1

Q ss_pred             CchhHHHHHHHHHhhCCCcc--eEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCC
Q 039644            1 IGKTAIARAIFDKISGDFEC--SCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVT   78 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~--~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~   78 (192)
                      +|||+|++.+++.+......  ++++           +..++...+...+.....   ....++..+++ .-+|||||+.
T Consensus       152 ~GKTHLl~Ai~~~l~~~~~~~~v~yv-----------~~~~f~~~~~~~l~~~~~---~~~~~~~~~~~-~dvLiIDDiq  216 (450)
T PRK14087        152 MGKTHLLKAAKNYIESNFSDLKVSYM-----------SGDEFARKAVDILQKTHK---EIEQFKNEICQ-NDVLIIDDVQ  216 (450)
T ss_pred             CcHHHHHHHHHHHHHHhCCCCeEEEE-----------EHHHHHHHHHHHHHHhhh---HHHHHHHHhcc-CCEEEEeccc
Confidence            69999999999976543322  2333           345666666665543211   23344444443 3378889997


Q ss_pred             Cch---h-HHHhhccCCC-CCCCceEEEEecchh---------HHhhcCCCceEecCCCCHHHHHHHHHHhhcCCCCCCc
Q 039644           79 CFS---Q-LESLMGSLDW-LTPVSRIILTTRNKQ---------VLRNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDV  144 (192)
Q Consensus        79 ~~~---~-~~~l~~~~~~-~~~~~~iivTtR~~~---------~~~~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~  144 (192)
                      ...   . .+.+...+.. ...+..||+|+....         +...+..+-...+++++.++-.+++.+.+-.......
T Consensus       217 ~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l~~l~~rL~SR~~~Gl~~~L~~pd~e~r~~iL~~~~~~~gl~~~  296 (450)
T PRK14087        217 FLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELLNGFDNRLITRFNMGLSIAIQKLDNKTATAIIKKEIKNQNIKQE  296 (450)
T ss_pred             cccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHHhhccHHHHHHHhCCceeccCCcCHHHHHHHHHHHHHhcCCCCC
Confidence            432   1 2233222211 124456888865432         2222344567889999999999999887743221113


Q ss_pred             cHHHHHHHHHHHhCCCchHHHHHH
Q 039644          145 GYEKLSSNVTKYAQGIPLALKVLS  168 (192)
Q Consensus       145 ~~~~~~~~i~~~~~g~Plai~~~~  168 (192)
                      -.++...-|++.+.|.|..+.-+.
T Consensus       297 l~~evl~~Ia~~~~gd~R~L~gaL  320 (450)
T PRK14087        297 VTEEAINFISNYYSDDVRKIKGSV  320 (450)
T ss_pred             CCHHHHHHHHHccCCCHHHHHHHH
Confidence            345667778888888888766555

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.13  E-value=5.4e-05  Score=56.23  Aligned_cols=140  Identities=15%  Similarity=0.201  Sum_probs=78.3

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||+||+.++++..+.....++++ ...       +......+                 ...+.. .-+|||||++..
T Consensus        49 ~GKT~la~~~~~~~~~~~~~~~~i~-~~~-------~~~~~~~~-----------------~~~~~~-~~lLvIDdi~~l  102 (226)
T TIGR03420        49 SGKSHLLQAACAAAEERGKSAIYLP-LAE-------LAQADPEV-----------------LEGLEQ-ADLVCLDDVEAI  102 (226)
T ss_pred             CCHHHHHHHHHHHHHhcCCcEEEEe-HHH-------HHHhHHHH-----------------Hhhccc-CCEEEEeChhhh
Confidence            6999999999997655544555665 222       11100111                 111222 238999999854


Q ss_pred             h---hH-HHhhccCCC-CCCCceEEEEecchh---------HHhhcCCCceEecCCCCHHHHHHHHHHhhcCCCCCCccH
Q 039644           81 S---QL-ESLMGSLDW-LTPVSRIILTTRNKQ---------VLRNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGY  146 (192)
Q Consensus        81 ~---~~-~~l~~~~~~-~~~~~~iivTtR~~~---------~~~~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~  146 (192)
                      .   .| +.+...+.. ...+..+|+||+...         ..........+.+++++.++...++...+-...  -.-.
T Consensus       103 ~~~~~~~~~L~~~l~~~~~~~~~iIits~~~~~~~~~~~~~L~~r~~~~~~i~l~~l~~~e~~~~l~~~~~~~~--~~~~  180 (226)
T TIGR03420       103 AGQPEWQEALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPDLRTRLAWGLVFQLPPLSDEEKIAALQSRAARRG--LQLP  180 (226)
T ss_pred             cCChHHHHHHHHHHHHHHHcCCeEEEECCCChHHCCcccHHHHHHHhcCeeEecCCCCHHHHHHHHHHHHHHcC--CCCC
Confidence            3   22 223222211 123347888887532         122222245789999999998888876542211  1223


Q ss_pred             HHHHHHHHHHhCCCchHHHHHH
Q 039644          147 EKLSSNVTKYAQGIPLALKVLS  168 (192)
Q Consensus       147 ~~~~~~i~~~~~g~Plai~~~~  168 (192)
                      .+....+.+.+.|.|..+.-+.
T Consensus       181 ~~~l~~L~~~~~gn~r~L~~~l  202 (226)
T TIGR03420       181 DEVADYLLRHGSRDMGSLMALL  202 (226)
T ss_pred             HHHHHHHHHhccCCHHHHHHHH
Confidence            4455667777888887766554

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.

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.12  E-value=0.00011  Score=59.71  Aligned_cols=143  Identities=17%  Similarity=0.259  Sum_probs=80.6

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +||||||+.+++.....|..   +. ...     ....++ +.+++....            ....+++.+|+||+++..
T Consensus        47 tGKTtLA~~ia~~~~~~~~~---l~-a~~-----~~~~~i-r~ii~~~~~------------~~~~g~~~vL~IDEi~~l  104 (413)
T PRK13342         47 TGKTTLARIIAGATDAPFEA---LS-AVT-----SGVKDL-REVIEEARQ------------RRSAGRRTILFIDEIHRF  104 (413)
T ss_pred             CCHHHHHHHHHHHhCCCEEE---Ee-ccc-----ccHHHH-HHHHHHHHH------------hhhcCCceEEEEechhhh
Confidence            69999999999977654422   11 110     122222 222222211            011356789999999865


Q ss_pred             h--hHHHhhccCCCCCCCceEEEE--ecchhHH---hhcCCCceEecCCCCHHHHHHHHHHhhcCCCCCC-ccHHHHHHH
Q 039644           81 S--QLESLMGSLDWLTPVSRIILT--TRNKQVL---RNWGVSKIYEMEALEYHHALELFSQHAFKRNHPD-VGYEKLSSN  152 (192)
Q Consensus        81 ~--~~~~l~~~~~~~~~~~~iivT--tR~~~~~---~~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~-~~~~~~~~~  152 (192)
                      .  +.+.+...+.   .+..+++.  |.+....   ...+....+.+.+++.++...++.+......... ....+....
T Consensus       105 ~~~~q~~LL~~le---~~~iilI~att~n~~~~l~~aL~SR~~~~~~~~ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~  181 (413)
T PRK13342        105 NKAQQDALLPHVE---DGTITLIGATTENPSFEVNPALLSRAQVFELKPLSEEDIEQLLKRALEDKERGLVELDDEALDA  181 (413)
T ss_pred             CHHHHHHHHHHhh---cCcEEEEEeCCCChhhhccHHHhccceeeEeCCCCHHHHHHHHHHHHHHhhcCCCCCCHHHHHH
Confidence            3  3455554443   24444443  3333211   1113346899999999999999987653211111 233556778


Q ss_pred             HHHHhCCCchHHHHHH
Q 039644          153 VTKYAQGIPLALKVLS  168 (192)
Q Consensus       153 i~~~~~g~Plai~~~~  168 (192)
                      +++.++|.+..+..+.
T Consensus       182 l~~~s~Gd~R~aln~L  197 (413)
T PRK13342        182 LARLANGDARRALNLL  197 (413)
T ss_pred             HHHhCCCCHHHHHHHH
Confidence            8888999887654443

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=98.12  E-value=0.00029  Score=55.19  Aligned_cols=141  Identities=18%  Similarity=0.224  Sum_probs=85.6

Q ss_pred             CchhHHHHHHHHHhh------CCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEE
Q 039644            1 IGKTAIARAIFDKIS------GDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVF   74 (192)
Q Consensus         1 iGKTtLa~~~~~~~~------~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVl   74 (192)
                      +|||++|+.+++.+-      .|.+...|.. ...  .. ..+.++. ++.+.+...+            ..+++-++|+
T Consensus        37 ~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~-~~~--~~-i~v~~ir-~~~~~~~~~p------------~~~~~kv~iI   99 (313)
T PRK05564         37 IGKSLLAKEIALKILGKSQQREYVDIIEFKP-INK--KS-IGVDDIR-NIIEEVNKKP------------YEGDKKVIII   99 (313)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCCCCeEEecc-ccC--CC-CCHHHHH-HHHHHHhcCc------------ccCCceEEEE
Confidence            599999999999642      2333333432 111  11 2333432 3333332211            1245557788


Q ss_pred             eCCCCc--hhHHHhhccCCCCCCCceEEEEecchhHHhh--cCCCceEecCCCCHHHHHHHHHHhhcCCCCCCccHHHHH
Q 039644           75 DDVTCF--SQLESLMGSLDWLTPVSRIILTTRNKQVLRN--WGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLS  150 (192)
Q Consensus        75 Ddv~~~--~~~~~l~~~~~~~~~~~~iivTtR~~~~~~~--~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~  150 (192)
                      |+++..  ..++.+...+.+...++.+|++|.+......  -+....+.+.+++.++....+......      ...+.+
T Consensus       100 ~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~~ll~TI~SRc~~~~~~~~~~~~~~~~l~~~~~~------~~~~~~  173 (313)
T PRK05564        100 YNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRCQIYKLNRLSKEEIEKFISYKYND------IKEEEK  173 (313)
T ss_pred             echhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHHhhceeeeCCCcCHHHHHHHHHHHhcC------CCHHHH
Confidence            887654  4588888888877788999988876543221  144678999999999988877654311      112335


Q ss_pred             HHHHHHhCCCchHH
Q 039644          151 SNVTKYAQGIPLAL  164 (192)
Q Consensus       151 ~~i~~~~~g~Plai  164 (192)
                      ..++..++|.|.-+
T Consensus       174 ~~l~~~~~g~~~~a  187 (313)
T PRK05564        174 KSAIAFSDGIPGKV  187 (313)
T ss_pred             HHHHHHcCCCHHHH
Confidence            67788888887544

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.11  E-value=0.00011  Score=62.19  Aligned_cols=98  Identities=11%  Similarity=0.080  Sum_probs=64.8

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      ++.-++|||+++...  .++.|...+.....++++|++|.+.. +...+ +....+.++.++.++..+.+.+.+..... 
T Consensus       123 gr~KViIIDEah~Ls~~AaNALLKTLEEPP~~v~FILaTtep~kLlpTIrSRCq~f~f~~ls~eei~~~L~~Il~~Egi-  201 (700)
T PRK12323        123 GRFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPGHIVSHLDAILGEEGI-  201 (700)
T ss_pred             CCceEEEEEChHhcCHHHHHHHHHhhccCCCCceEEEEeCChHhhhhHHHHHHHhcccCCCChHHHHHHHHHHHHHcCC-
Confidence            455699999999664  47777776666556677777666543 22222 44578999999999999888876532221 


Q ss_pred             CccHHHHHHHHHHHhCCCchHHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLALKV  166 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai~~  166 (192)
                       ....+....|++.++|.|.....
T Consensus       202 -~~d~eAL~~IA~~A~Gs~RdALs  224 (700)
T PRK12323        202 -AHEVNALRLLAQAAQGSMRDALS  224 (700)
T ss_pred             -CCCHHHHHHHHHHcCCCHHHHHH
Confidence             12234456788889988864433

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=98.10  E-value=0.00011  Score=63.10  Aligned_cols=98  Identities=14%  Similarity=0.158  Sum_probs=64.9

Q ss_pred             CceEEEEEeCCCCchh--HHHhhccCCCCCCCceEEEEecchhHHhh--cCCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFSQ--LESLMGSLDWLTPVSRIILTTRNKQVLRN--WGVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~~--~~~l~~~~~~~~~~~~iivTtR~~~~~~~--~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      ++.-++|||+++....  ++.+...+......+++|++|++......  .+....+.++.++.++..+.+.+......  
T Consensus       118 gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~FILaTtd~~KIp~TIrSRCq~f~Fk~Ls~eeIv~~L~~Il~~Eg--  195 (830)
T PRK07003        118 ARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQKIPVTVLSRCLQFNLKQMPAGHIVSHLERILGEER--  195 (830)
T ss_pred             CCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeEEEEEECChhhccchhhhheEEEecCCcCHHHHHHHHHHHHHHcC--
Confidence            3445899999997654  77777666555567888888877553321  14467899999999999998887653222  


Q ss_pred             CccHHHHHHHHHHHhCCCch-HHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPL-ALKV  166 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Pl-ai~~  166 (192)
                      -....+....|++.++|... |+.+
T Consensus       196 I~id~eAL~lIA~~A~GsmRdALsL  220 (830)
T PRK07003        196 IAFEPQALRLLARAAQGSMRDALSL  220 (830)
T ss_pred             CCCCHHHHHHHHHHcCCCHHHHHHH
Confidence            11234455667777777553 4443

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.08  E-value=0.00027  Score=56.48  Aligned_cols=95  Identities=13%  Similarity=0.132  Sum_probs=62.1

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      ++.-++|+|+++...  .++.+...+......+++|++|.+.. +.... +....+++.+++.++..+.+...+....  
T Consensus       118 ~~~kviIIDEa~~l~~~a~naLLk~lEe~~~~~~fIl~t~~~~~l~~tI~SRc~~~~~~~l~~~el~~~L~~~~~~~g--  195 (363)
T PRK14961        118 SRFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEKIPKTILSRCLQFKLKIISEEKIFNFLKYILIKES--  195 (363)
T ss_pred             CCceEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEcCChHhhhHHHHhhceEEeCCCCCHHHHHHHHHHHHHHcC--
Confidence            345699999998765  36667666665556667777765533 22222 4457899999999999888776553221  


Q ss_pred             CccHHHHHHHHHHHhCCCchH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Pla  163 (192)
                      ..-.++....|++.++|.|..
T Consensus       196 ~~i~~~al~~ia~~s~G~~R~  216 (363)
T PRK14961        196 IDTDEYALKLIAYHAHGSMRD  216 (363)
T ss_pred             CCCCHHHHHHHHHHcCCCHHH
Confidence            112334566778888887763

>PRK08727 hypothetical protein; Validated

Probab=98.05  E-value=9.6e-05  Score=55.41  Aligned_cols=136  Identities=15%  Similarity=0.104  Sum_probs=78.3

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||+|+..+++...+......|+.. ..       ....+...++                 .+ ...-+|||||++..
T Consensus        52 ~GKThL~~a~~~~~~~~~~~~~y~~~-~~-------~~~~~~~~~~-----------------~l-~~~dlLiIDDi~~l  105 (233)
T PRK08727         52 TGKTHLALALCAAAEQAGRSSAYLPL-QA-------AAGRLRDALE-----------------AL-EGRSLVALDGLESI  105 (233)
T ss_pred             CCHHHHHHHHHHHHHHcCCcEEEEeH-HH-------hhhhHHHHHH-----------------HH-hcCCEEEEeCcccc
Confidence            69999999999986655455566652 11       1111111111                 11 12248999999743


Q ss_pred             h---hHH-HhhccCCC-CCCCceEEEEecchh---------HHhhcCCCceEecCCCCHHHHHHHHHHhhcCCCCCCccH
Q 039644           81 S---QLE-SLMGSLDW-LTPVSRIILTTRNKQ---------VLRNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGY  146 (192)
Q Consensus        81 ~---~~~-~l~~~~~~-~~~~~~iivTtR~~~---------~~~~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~  146 (192)
                      .   .+. .+...+.. ...+..+|+||+...         ....+.....+++++++.++-..++.+.+....  -.-.
T Consensus       106 ~~~~~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~l~~~~~dL~SRl~~~~~~~l~~~~~e~~~~iL~~~a~~~~--l~l~  183 (233)
T PRK08727        106 AGQREDEVALFDFHNRARAAGITLLYTARQMPDGLALVLPDLRSRLAQCIRIGLPVLDDVARAAVLRERAQRRG--LALD  183 (233)
T ss_pred             cCChHHHHHHHHHHHHHHHcCCeEEEECCCChhhhhhhhHHHHHHHhcCceEEecCCCHHHHHHHHHHHHHHcC--CCCC
Confidence            2   232 22221111 124566999987532         222223356899999999999999998664322  2233


Q ss_pred             HHHHHHHHHHhCCCchHH
Q 039644          147 EKLSSNVTKYAQGIPLAL  164 (192)
Q Consensus       147 ~~~~~~i~~~~~g~Plai  164 (192)
                      ++...-|++.+.|..-.+
T Consensus       184 ~e~~~~La~~~~rd~r~~  201 (233)
T PRK08727        184 EAAIDWLLTHGERELAGL  201 (233)
T ss_pred             HHHHHHHHHhCCCCHHHH
Confidence            455667777787665554

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.03  E-value=0.00017  Score=63.01  Aligned_cols=98  Identities=12%  Similarity=0.069  Sum_probs=64.5

Q ss_pred             CCceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCC
Q 039644           66 SRMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNH  141 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~  141 (192)
                      .++.-++|||+++...  .++.|+..+-......++|++|.+.. +...+ .....+.+++++.++....+.+.+.... 
T Consensus       117 ~gk~KViIIDEAh~LT~eAqNALLKtLEEPP~~vrFILaTTe~~kLl~TIlSRCq~f~fkpLs~eEI~~~L~~il~~Eg-  195 (944)
T PRK14949        117 RGRFKVYLIDEVHMLSRSSFNALLKTLEEPPEHVKFLLATTDPQKLPVTVLSRCLQFNLKSLTQDEIGTQLNHILTQEQ-  195 (944)
T ss_pred             cCCcEEEEEechHhcCHHHHHHHHHHHhccCCCeEEEEECCCchhchHHHHHhheEEeCCCCCHHHHHHHHHHHHHHcC-
Confidence            3556699999998653  46777666655555666777665433 22221 4457899999999999988877653211 


Q ss_pred             CCccHHHHHHHHHHHhCCCchHHH
Q 039644          142 PDVGYEKLSSNVTKYAQGIPLALK  165 (192)
Q Consensus       142 ~~~~~~~~~~~i~~~~~g~Plai~  165 (192)
                       -....+....|++.++|.|.-+.
T Consensus       196 -I~~edeAL~lIA~~S~Gd~R~AL  218 (944)
T PRK14949        196 -LPFEAEALTLLAKAANGSMRDAL  218 (944)
T ss_pred             -CCCCHHHHHHHHHHcCCCHHHHH
Confidence             12234556678888888876443

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

Probab=97.96  E-value=0.00014  Score=54.04  Aligned_cols=145  Identities=14%  Similarity=0.196  Sum_probs=79.6

Q ss_pred             CchhHHHHHHHHHhhCCCcc--eEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCC
Q 039644            1 IGKTAIARAIFDKISGDFEC--SCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVT   78 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~--~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~   78 (192)
                      +|||.|...+++.+.+..+.  ++++           +..++...+...+...     ....++..+++-. +|+|||++
T Consensus        45 ~GKTHLL~Ai~~~~~~~~~~~~v~y~-----------~~~~f~~~~~~~~~~~-----~~~~~~~~~~~~D-lL~iDDi~  107 (219)
T PF00308_consen   45 LGKTHLLQAIANEAQKQHPGKRVVYL-----------SAEEFIREFADALRDG-----EIEEFKDRLRSAD-LLIIDDIQ  107 (219)
T ss_dssp             SSHHHHHHHHHHHHHHHCTTS-EEEE-----------EHHHHHHHHHHHHHTT-----SHHHHHHHHCTSS-EEEEETGG
T ss_pred             CCHHHHHHHHHHHHHhccccccceee-----------cHHHHHHHHHHHHHcc-----cchhhhhhhhcCC-EEEEecch
Confidence            59999999999987654443  3444           3456666665555442     3344555666433 68899997


Q ss_pred             Cch---hHH-HhhccCCC-CCCCceEEEEecchh---------HHhhcCCCceEecCCCCHHHHHHHHHHhhcCCCCCCc
Q 039644           79 CFS---QLE-SLMGSLDW-LTPVSRIILTTRNKQ---------VLRNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDV  144 (192)
Q Consensus        79 ~~~---~~~-~l~~~~~~-~~~~~~iivTtR~~~---------~~~~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~  144 (192)
                      ...   .|. .+...+.. ...|.++|+|++...         .......+-.+++++.+.++-..++.+.+....-  .
T Consensus       108 ~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~~~~L~SRl~~Gl~~~l~~pd~~~r~~il~~~a~~~~~--~  185 (219)
T PF00308_consen  108 FLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSELSGLLPDLRSRLSWGLVVELQPPDDEDRRRILQKKAKERGI--E  185 (219)
T ss_dssp             GGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS-HHHHHHHHCSEEEEE----HHHHHHHHHHHHHHTT----
T ss_pred             hhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccccccChhhhhhHhhcchhhcCCCCHHHHHHHHHHHHHHhCC--C
Confidence            542   122 22211111 135678999995532         2222244567889999999999998887743222  1


Q ss_pred             cHHHHHHHHHHHhCCCchHH
Q 039644          145 GYEKLSSNVTKYAQGIPLAL  164 (192)
Q Consensus       145 ~~~~~~~~i~~~~~g~Plai  164 (192)
                      -.++...-|.+.+.+..-.+
T Consensus       186 l~~~v~~~l~~~~~~~~r~L  205 (219)
T PF00308_consen  186 LPEEVIEYLARRFRRDVREL  205 (219)
T ss_dssp             S-HHHHHHHHHHTTSSHHHH
T ss_pred             CcHHHHHHHHHhhcCCHHHH
Confidence            23344455555555444433

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.

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=97.95  E-value=0.00011  Score=57.13  Aligned_cols=54  Identities=17%  Similarity=0.064  Sum_probs=39.6

Q ss_pred             CceEecCCCCHHHHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCCchHHHHHHHH
Q 039644          115 SKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCF  170 (192)
Q Consensus       115 ~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plai~~~~~~  170 (192)
                      ...+.+++++.++..+++.+.+....  ..-.++....|++.|+|.|..+..++..
T Consensus       151 ~~~~~l~~l~~~e~~~il~~~~~~~~--~~~~~~al~~ia~~~~G~pR~~~~ll~~  204 (305)
T TIGR00635       151 GIILRLEFYTVEELAEIVSRSAGLLN--VEIEPEAALEIARRSRGTPRIANRLLRR  204 (305)
T ss_pred             ceEEEeCCCCHHHHHHHHHHHHHHhC--CCcCHHHHHHHHHHhCCCcchHHHHHHH
Confidence            34678999999999999998775322  2233556778999999999876555543

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.

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

Probab=97.95  E-value=3e-05  Score=52.44  Aligned_cols=98  Identities=18%  Similarity=0.201  Sum_probs=64.9

Q ss_pred             CchhHHHHHHHHHhhCC-----CcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-cC---chHHHHhhcCCc-eE
Q 039644            1 IGKTAIARAIFDKISGD-----FECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV-MP---YIDLNFRRLSRM-KV   70 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~-----F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~---~~~~l~~~l~~~-~~   70 (192)
                      +|||+++..+++.....     -..++|+.....     .+...+...++..+...... ..   ..+.+...+... ..
T Consensus        15 ~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~l~~~~~~   89 (131)
T PF13401_consen   15 SGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSS-----RTPRDFAQEILEALGLPLKSRQTSDELRSLLIDALDRRRVV   89 (131)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHH-----SSHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHHHHHHCTEE
T ss_pred             CCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCC-----CCHHHHHHHHHHHhCccccccCCHHHHHHHHHHHHHhcCCe
Confidence            69999999999976432     245567763333     47889999999999866554 22   556666666544 46


Q ss_pred             EEEEeCCCCc-h--hHHHhhccCCCCCCCceEEEEecc
Q 039644           71 LIVFDDVTCF-S--QLESLMGSLDWLTPVSRIILTTRN  105 (192)
Q Consensus        71 LlVlDdv~~~-~--~~~~l~~~~~~~~~~~~iivTtR~  105 (192)
                      +||+|+++.. .  .++.+.... + ..+.++|+..+.
T Consensus        90 ~lviDe~~~l~~~~~l~~l~~l~-~-~~~~~vvl~G~~  125 (131)
T PF13401_consen   90 LLVIDEADHLFSDEFLEFLRSLL-N-ESNIKVVLVGTP  125 (131)
T ss_dssp             EEEEETTHHHHTHHHHHHHHHHT-C-SCBEEEEEEESS
T ss_pred             EEEEeChHhcCCHHHHHHHHHHH-h-CCCCeEEEEECh
Confidence            9999999865 3  244443322 2 566677777654

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.92  E-value=0.00045  Score=58.71  Aligned_cols=96  Identities=14%  Similarity=0.122  Sum_probs=62.8

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchhHHh-h-cCCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQVLR-N-WGVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~~~~-~-~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      ++.-++|+|+++...  ..+.+...+.....+.++|++|.+..... . .+....+++.+++.++....+...+....  
T Consensus       117 gk~KV~IIDEVh~LS~~A~NALLKtLEEPP~~v~FILaTtd~~kIp~TIlSRCq~feFkpLs~eEI~k~L~~Il~kEg--  194 (702)
T PRK14960        117 GRFKVYLIDEVHMLSTHSFNALLKTLEEPPEHVKFLFATTDPQKLPITVISRCLQFTLRPLAVDEITKHLGAILEKEQ--  194 (702)
T ss_pred             CCcEEEEEechHhcCHHHHHHHHHHHhcCCCCcEEEEEECChHhhhHHHHHhhheeeccCCCHHHHHHHHHHHHHHcC--
Confidence            455689999998653  46667666655556677888776543221 1 14567899999999999888877653322  


Q ss_pred             CccHHHHHHHHHHHhCCCchHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLAL  164 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai  164 (192)
                      -....+....|++.++|.+..+
T Consensus       195 I~id~eAL~~IA~~S~GdLRdA  216 (702)
T PRK14960        195 IAADQDAIWQIAESAQGSLRDA  216 (702)
T ss_pred             CCCCHHHHHHHHHHcCCCHHHH
Confidence            1223445566777777776443

>PRK09087 hypothetical protein; Validated

Probab=97.91  E-value=0.0009  Score=49.95  Aligned_cols=112  Identities=10%  Similarity=0.102  Sum_probs=68.2

Q ss_pred             EEEEeCCCCch----hHHHhhccCCCCCCCceEEEEecc---------hhHHhhcCCCceEecCCCCHHHHHHHHHHhhc
Q 039644           71 LIVFDDVTCFS----QLESLMGSLDWLTPVSRIILTTRN---------KQVLRNWGVSKIYEMEALEYHHALELFSQHAF  137 (192)
Q Consensus        71 LlVlDdv~~~~----~~~~l~~~~~~~~~~~~iivTtR~---------~~~~~~~~~~~~~~l~~l~~~ea~~lf~~~~~  137 (192)
                      ++++||++...    .+-.+...+.  ..|..+|+|++.         +.....+.....+++++++.++-.+++.+.+-
T Consensus        90 ~l~iDDi~~~~~~~~~lf~l~n~~~--~~g~~ilits~~~p~~~~~~~~dL~SRl~~gl~~~l~~pd~e~~~~iL~~~~~  167 (226)
T PRK09087         90 PVLIEDIDAGGFDETGLFHLINSVR--QAGTSLLMTSRLWPSSWNVKLPDLKSRLKAATVVEIGEPDDALLSQVIFKLFA  167 (226)
T ss_pred             eEEEECCCCCCCCHHHHHHHHHHHH--hCCCeEEEECCCChHHhccccccHHHHHhCCceeecCCCCHHHHHHHHHHHHH
Confidence            78889996431    2222222222  346679998863         33444445668899999999999999998774


Q ss_pred             CCCCCCccHHHHHHHHHHHhCCCchHHHHHHHHh------ccCC--HHHHHHHHHHH
Q 039644          138 KRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFL------HKRE--KEVWESAIDKL  186 (192)
Q Consensus       138 ~~~~~~~~~~~~~~~i~~~~~g~Plai~~~~~~l------~~~~--~~~w~~~l~~l  186 (192)
                      ...  -.-.++...-|++.+.|..-++..+-..|      ..+.  ....+++++.+
T Consensus       168 ~~~--~~l~~ev~~~La~~~~r~~~~l~~~l~~L~~~~~~~~~~it~~~~~~~l~~~  222 (226)
T PRK09087        168 DRQ--LYVDPHVVYYLVSRMERSLFAAQTIVDRLDRLALERKSRITRALAAEVLNEM  222 (226)
T ss_pred             HcC--CCCCHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHhh
Confidence            322  12234556667777777766655432222      2222  67777777654

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=97.89  E-value=0.001  Score=55.35  Aligned_cols=95  Identities=13%  Similarity=0.203  Sum_probs=62.0

Q ss_pred             CceEEEEEeCCCCc--hhHHHhhccCCCCCCCceEEEEe-cchhHHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCF--SQLESLMGSLDWLTPVSRIILTT-RNKQVLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~iivTt-R~~~~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +++-++|+|+++..  ..++.+...+......+.+|+.| +...+.... +....+.+.+++.++....+...+..... 
T Consensus       127 ~~~KVvIIDEa~~Ls~~a~naLLk~LEepp~~~vfI~aTte~~kI~~tI~SRc~~~ef~~ls~~el~~~L~~i~~~egi-  205 (507)
T PRK06645        127 GKHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQKIPATIISRCQRYDLRRLSFEEIFKLLEYITKQENL-  205 (507)
T ss_pred             CCcEEEEEEChhhcCHHHHHHHHHHHhhcCCCEEEEEEeCChHHhhHHHHhcceEEEccCCCHHHHHHHHHHHHHHcCC-
Confidence            45668999999864  45777777766555666666554 333333322 44567999999999999988877643221 


Q ss_pred             CccHHHHHHHHHHHhCCCchH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Pla  163 (192)
                       ....+....|++.++|.+.-
T Consensus       206 -~ie~eAL~~Ia~~s~GslR~  225 (507)
T PRK06645        206 -KTDIEALRIIAYKSEGSARD  225 (507)
T ss_pred             -CCCHHHHHHHHHHcCCCHHH
Confidence             12234456677788877644

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.87  E-value=0.00089  Score=55.76  Aligned_cols=96  Identities=11%  Similarity=0.106  Sum_probs=62.4

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +++-++|+|+++...  .++.+...+......+.+|++|.... +.... +....+.+.+++.++..+.+...+-.... 
T Consensus       115 ~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~~~~kl~~~I~SRc~~~~f~~ls~~el~~~L~~i~~~egi-  193 (504)
T PRK14963        115 GGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTILSRTQHFRFRRLTEEEIAGKLRRLLEAEGR-  193 (504)
T ss_pred             CCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcCChhhCChHHhcceEEEEecCCCHHHHHHHHHHHHHHcCC-
Confidence            456699999998653  46777766665555566666665432 22222 44568999999999999998876633221 


Q ss_pred             CccHHHHHHHHHHHhCCCchHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLAL  164 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai  164 (192)
                       ....+....|++.++|.+--+
T Consensus       194 -~i~~~Al~~ia~~s~GdlR~a  214 (504)
T PRK14963        194 -EAEPEALQLVARLADGAMRDA  214 (504)
T ss_pred             -CCCHHHHHHHHHHcCCCHHHH
Confidence             123445667788888877544

>PRK08084 DNA replication initiation factor; Provisional

Probab=97.87  E-value=0.00045  Score=51.85  Aligned_cols=140  Identities=14%  Similarity=0.180  Sum_probs=78.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||+|+..+++.....-..+.++. ...       .......                 +.+.+.. --++++||+...
T Consensus        56 ~GKThLl~a~~~~~~~~~~~v~y~~-~~~-------~~~~~~~-----------------~~~~~~~-~dlliiDdi~~~  109 (235)
T PRK08084         56 AGRSHLLHAACAELSQRGRAVGYVP-LDK-------RAWFVPE-----------------VLEGMEQ-LSLVCIDNIECI  109 (235)
T ss_pred             CCHHHHHHHHHHHHHhCCCeEEEEE-HHH-------HhhhhHH-----------------HHHHhhh-CCEEEEeChhhh
Confidence            6999999999997655434455655 211       0000001                 1111111 137999999753


Q ss_pred             ---hhHHHhh-ccCCC-CCCC-ceEEEEecchh---------HHhhcCCCceEecCCCCHHHHHHHHHHhhcCCCCCCcc
Q 039644           81 ---SQLESLM-GSLDW-LTPV-SRIILTTRNKQ---------VLRNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVG  145 (192)
Q Consensus        81 ---~~~~~l~-~~~~~-~~~~-~~iivTtR~~~---------~~~~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~  145 (192)
                         ..|+... ..+.. ...| .++|+||+...         ....+....++.+++++.++-.+++.+.+....  -.-
T Consensus       110 ~~~~~~~~~lf~l~n~~~e~g~~~li~ts~~~p~~l~~~~~~L~SRl~~g~~~~l~~~~~~~~~~~l~~~a~~~~--~~l  187 (235)
T PRK08084        110 AGDELWEMAIFDLYNRILESGRTRLLITGDRPPRQLNLGLPDLASRLDWGQIYKLQPLSDEEKLQALQLRARLRG--FEL  187 (235)
T ss_pred             cCCHHHHHHHHHHHHHHHHcCCCeEEEeCCCChHHcCcccHHHHHHHhCCceeeecCCCHHHHHHHHHHHHHHcC--CCC
Confidence               2343221 11111 1123 47999987543         333334567899999999999998887553321  223


Q ss_pred             HHHHHHHHHHHhCCCchHHHHHH
Q 039644          146 YEKLSSNVTKYAQGIPLALKVLS  168 (192)
Q Consensus       146 ~~~~~~~i~~~~~g~Plai~~~~  168 (192)
                      .++...-|++.+.|..-++..+-
T Consensus       188 ~~~v~~~L~~~~~~d~r~l~~~l  210 (235)
T PRK08084        188 PEDVGRFLLKRLDREMRTLFMTL  210 (235)
T ss_pred             CHHHHHHHHHhhcCCHHHHHHHH
Confidence            34556667777776665544443

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

Probab=97.86  E-value=0.00044  Score=55.91  Aligned_cols=62  Identities=19%  Similarity=0.248  Sum_probs=49.0

Q ss_pred             ceEEEEEeCCCCchhHHHhhccCCCCCCCceEEEEecchhHHhhc------CCCceEecCCCCHHHHHH
Q 039644           68 MKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNW------GVSKIYEMEALEYHHALE  130 (192)
Q Consensus        68 ~~~LlVlDdv~~~~~~~~l~~~~~~~~~~~~iivTtR~~~~~~~~------~~~~~~~l~~l~~~ea~~  130 (192)
                      ++..|+||.|.....|......+.+.+.. +|++|+.+.......      |....+.+-||+..|-..
T Consensus        94 ~~~yifLDEIq~v~~W~~~lk~l~d~~~~-~v~itgsss~ll~~~~~~~L~GR~~~~~l~PlSF~Efl~  161 (398)
T COG1373          94 EKSYIFLDEIQNVPDWERALKYLYDRGNL-DVLITGSSSSLLSKEISESLAGRGKDLELYPLSFREFLK  161 (398)
T ss_pred             CCceEEEecccCchhHHHHHHHHHccccc-eEEEECCchhhhccchhhhcCCCceeEEECCCCHHHHHh
Confidence            77899999999999999888887776665 889987765543332      556789999999999865

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=97.85  E-value=0.00026  Score=55.78  Aligned_cols=53  Identities=11%  Similarity=0.027  Sum_probs=39.7

Q ss_pred             CceEecCCCCHHHHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCCchHHHHHHH
Q 039644          115 SKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSC  169 (192)
Q Consensus       115 ~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plai~~~~~  169 (192)
                      ...+.+++++.++..+++.+.+....  ....++....|++.|+|.|..+..+..
T Consensus       172 ~~~~~l~~~~~~e~~~il~~~~~~~~--~~~~~~~~~~ia~~~~G~pR~a~~~l~  224 (328)
T PRK00080        172 GIVQRLEFYTVEELEKIVKRSARILG--VEIDEEGALEIARRSRGTPRIANRLLR  224 (328)
T ss_pred             CeeeecCCCCHHHHHHHHHHHHHHcC--CCcCHHHHHHHHHHcCCCchHHHHHHH
Confidence            35689999999999999998875432  223456688999999999975555544

>PRK05642 DNA replication initiation factor; Validated

Probab=97.84  E-value=0.00043  Score=51.97  Aligned_cols=141  Identities=16%  Similarity=0.174  Sum_probs=79.3

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||.|+..+++.+...-..++|++ .          .++....              ..+.+.+.+-. +||+||+...
T Consensus        56 ~GKTHLl~a~~~~~~~~~~~v~y~~-~----------~~~~~~~--------------~~~~~~~~~~d-~LiiDDi~~~  109 (234)
T PRK05642         56 VGRSHLLQAACLRFEQRGEPAVYLP-L----------AELLDRG--------------PELLDNLEQYE-LVCLDDLDVI  109 (234)
T ss_pred             CCHHHHHHHHHHHHHhCCCcEEEee-H----------HHHHhhh--------------HHHHHhhhhCC-EEEEechhhh
Confidence            6999999999987654434556665 1          2222110              11222233222 6889999732


Q ss_pred             ---hhHHH-hhccCCC-CCCCceEEEEecchhHH---------hhcCCCceEecCCCCHHHHHHHHHHhhcCCCCCCccH
Q 039644           81 ---SQLES-LMGSLDW-LTPVSRIILTTRNKQVL---------RNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGY  146 (192)
Q Consensus        81 ---~~~~~-l~~~~~~-~~~~~~iivTtR~~~~~---------~~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~  146 (192)
                         ..|+. +...+.. ...|..+|+|++.....         ..+.....+.+++++.++-.++++..+....  -.-.
T Consensus       110 ~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~SRl~~gl~~~l~~~~~e~~~~il~~ka~~~~--~~l~  187 (234)
T PRK05642        110 AGKADWEEALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKSRLTLALVFQMRGLSDEDKLRALQLRASRRG--LHLT  187 (234)
T ss_pred             cCChHHHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHHHHhcCeeeecCCCCHHHHHHHHHHHHHHcC--CCCC
Confidence               23332 3322221 23466788888753322         1223346788999999999999885553321  1222


Q ss_pred             HHHHHHHHHHhCCCchHHHHHHH
Q 039644          147 EKLSSNVTKYAQGIPLALKVLSC  169 (192)
Q Consensus       147 ~~~~~~i~~~~~g~Plai~~~~~  169 (192)
                      ++...-|++.+.|..-.+..+-.
T Consensus       188 ~ev~~~L~~~~~~d~r~l~~~l~  210 (234)
T PRK05642        188 DEVGHFILTRGTRSMSALFDLLE  210 (234)
T ss_pred             HHHHHHHHHhcCCCHHHHHHHHH
Confidence            45666677777777655444433

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=97.83  E-value=0.00045  Score=58.87  Aligned_cols=97  Identities=12%  Similarity=0.092  Sum_probs=62.3

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      ++.-++|||+++...  ..+.+...+-.....+++|++|.+.. +...+ +....+.+++++.++....+....-...  
T Consensus       118 g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~~~kLl~TI~SRC~~~~f~~Ls~~ei~~~L~~il~~e~--  195 (647)
T PRK07994        118 GRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRQQLEHILQAEQ--  195 (647)
T ss_pred             CCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCCccccchHHHhhheEeeCCCCCHHHHHHHHHHHHHHcC--
Confidence            456699999998654  46777666555455666666655533 22221 4467899999999999988877552211  


Q ss_pred             CccHHHHHHHHHHHhCCCchHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLALK  165 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai~  165 (192)
                      -.........|++.++|.+..+.
T Consensus       196 i~~e~~aL~~Ia~~s~Gs~R~Al  218 (647)
T PRK07994        196 IPFEPRALQLLARAADGSMRDAL  218 (647)
T ss_pred             CCCCHHHHHHHHHHcCCCHHHHH
Confidence            11223455678888888776433

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=97.82  E-value=0.0015  Score=51.54  Aligned_cols=92  Identities=13%  Similarity=0.137  Sum_probs=60.6

Q ss_pred             ceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchhHHh-hc-CCCceEecCCCCHHHHHHHHHHhhcCCCCCC
Q 039644           68 MKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQVLR-NW-GVSKIYEMEALEYHHALELFSQHAFKRNHPD  143 (192)
Q Consensus        68 ~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~~~~-~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~  143 (192)
                      .+-++|+|+++...  ..+.+...+-.-..++.+|++|.+..... .+ +....+.+.+++.+++.+.+......     
T Consensus       106 ~~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~~ll~TI~SRc~~~~~~~~~~~~~~~~L~~~~~~-----  180 (328)
T PRK05707        106 GRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTIKSRCQQQACPLPSNEESLQWLQQALPE-----  180 (328)
T ss_pred             CCeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChhhCcHHHHhhceeeeCCCcCHHHHHHHHHHhccc-----
Confidence            44456789999664  46666666655556778888887754322 22 45677999999999999888765311     


Q ss_pred             ccHHHHHHHHHHHhCCCchHHH
Q 039644          144 VGYEKLSSNVTKYAQGIPLALK  165 (192)
Q Consensus       144 ~~~~~~~~~i~~~~~g~Plai~  165 (192)
                       ...+.+..++..++|.|+...
T Consensus       181 -~~~~~~~~~l~la~Gsp~~A~  201 (328)
T PRK05707        181 -SDERERIELLTLAGGSPLRAL  201 (328)
T ss_pred             -CChHHHHHHHHHcCCCHHHHH
Confidence             112334566788889887443

>PRK04132 replication factor C small subunit; Provisional

Probab=97.82  E-value=0.0015  Score=57.36  Aligned_cols=147  Identities=13%  Similarity=0.148  Sum_probs=88.3

Q ss_pred             CchhHHHHHHHHHh-hCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKI-SGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~-~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~   79 (192)
                      +||||+|..+++++ ...+...+.-.+.++.    .++. .++.+++......+.          -..+.-++|||+++.
T Consensus       577 lGKTT~A~ala~~l~g~~~~~~~lElNASd~----rgid-~IR~iIk~~a~~~~~----------~~~~~KVvIIDEaD~  641 (846)
T PRK04132        577 LHNTTAALALARELFGENWRHNFLELNASDE----RGIN-VIREKVKEFARTKPI----------GGASFKIIFLDEADA  641 (846)
T ss_pred             ccHHHHHHHHHHhhhcccccCeEEEEeCCCc----ccHH-HHHHHHHHHHhcCCc----------CCCCCEEEEEECccc
Confidence            59999999999985 3334332222223331    2333 344444443322210          012346999999997


Q ss_pred             ch--hHHHhhccCCCCCCCceEEEEecchhHHh-hc-CCCceEecCCCCHHHHHHHHHHhhcCCCCCCccHHHHHHHHHH
Q 039644           80 FS--QLESLMGSLDWLTPVSRIILTTRNKQVLR-NW-GVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTK  155 (192)
Q Consensus        80 ~~--~~~~l~~~~~~~~~~~~iivTtR~~~~~~-~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~  155 (192)
                      ..  ....+...+-.....+++|++|....-.. .. +....+.+.+++.++....+.+.+-...-  ...++....|++
T Consensus       642 Lt~~AQnALLk~lEep~~~~~FILi~N~~~kIi~tIrSRC~~i~F~~ls~~~i~~~L~~I~~~Egi--~i~~e~L~~Ia~  719 (846)
T PRK04132        642 LTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGL--ELTEEGLQAILY  719 (846)
T ss_pred             CCHHHHHHHHHHhhCCCCCeEEEEEeCChhhCchHHhhhceEEeCCCCCHHHHHHHHHHHHHhcCC--CCCHHHHHHHHH
Confidence            64  46666666655556778888776654222 21 45678999999999988887765532111  112446677888


Q ss_pred             HhCCCchHH
Q 039644          156 YAQGIPLAL  164 (192)
Q Consensus       156 ~~~g~Plai  164 (192)
                      .++|.+...
T Consensus       720 ~s~GDlR~A  728 (846)
T PRK04132        720 IAEGDMRRA  728 (846)
T ss_pred             HcCCCHHHH
Confidence            888877543

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=97.82  E-value=0.0015  Score=52.23  Aligned_cols=95  Identities=11%  Similarity=0.077  Sum_probs=63.3

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchhHHh-hc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQVLR-NW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~~~~-~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +.+-++|+|+++..+  ....+...+.....++.+|++|.+..... .. +....+.+.+++.++..+++......  . 
T Consensus       140 ~~~kVviIDead~m~~~aanaLLK~LEepp~~~~~IL~t~~~~~llpti~SRc~~i~l~~l~~~~i~~~L~~~~~~--~-  216 (365)
T PRK07471        140 GGWRVVIVDTADEMNANAANALLKVLEEPPARSLFLLVSHAPARLLPTIRSRCRKLRLRPLAPEDVIDALAAAGPD--L-  216 (365)
T ss_pred             CCCEEEEEechHhcCHHHHHHHHHHHhcCCCCeEEEEEECCchhchHHhhccceEEECCCCCHHHHHHHHHHhccc--C-
Confidence            456799999998654  35566655555445667788777654322 21 45678999999999999998775411  1 


Q ss_pred             CccHHHHHHHHHHHhCCCchHHHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLALKVL  167 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai~~~  167 (192)
                         .......++..++|.|+....+
T Consensus       217 ---~~~~~~~l~~~s~Gsp~~Al~l  238 (365)
T PRK07471        217 ---PDDPRAALAALAEGSVGRALRL  238 (365)
T ss_pred             ---CHHHHHHHHHHcCCCHHHHHHH
Confidence               1122256788899999855444

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.81  E-value=0.00045  Score=56.03  Aligned_cols=144  Identities=12%  Similarity=0.172  Sum_probs=80.5

Q ss_pred             CchhHHHHHHHHHhhCCCcc--eEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCC
Q 039644            1 IGKTAIARAIFDKISGDFEC--SCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVT   78 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~--~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~   78 (192)
                      +|||+|++.+++.+.+..+.  ++++.           ..++...+...+...     ....+...+++ .-+|+|||++
T Consensus       147 ~GKThL~~ai~~~l~~~~~~~~v~yi~-----------~~~~~~~~~~~~~~~-----~~~~~~~~~~~-~dlLiiDDi~  209 (405)
T TIGR00362       147 LGKTHLLHAIGNEILENNPNAKVVYVS-----------SEKFTNDFVNALRNN-----KMEEFKEKYRS-VDLLLIDDIQ  209 (405)
T ss_pred             CcHHHHHHHHHHHHHHhCCCCcEEEEE-----------HHHHHHHHHHHHHcC-----CHHHHHHHHHh-CCEEEEehhh
Confidence            69999999999987665432  34443           334444555444322     22334444433 3388999997


Q ss_pred             Cch---hH-HHhhccCCC-CCCCceEEEEecchh---------HHhhcCCCceEecCCCCHHHHHHHHHHhhcCCCCCCc
Q 039644           79 CFS---QL-ESLMGSLDW-LTPVSRIILTTRNKQ---------VLRNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDV  144 (192)
Q Consensus        79 ~~~---~~-~~l~~~~~~-~~~~~~iivTtR~~~---------~~~~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~  144 (192)
                      ...   .+ +.+...+.. ...+..+|+|+....         +...+..+..+.+++.+.++-..++.+.+....  -.
T Consensus       210 ~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~SRl~~g~~v~i~~pd~~~r~~il~~~~~~~~--~~  287 (405)
T TIGR00362       210 FLAGKERTQEEFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRSRFEWGLVVDIEPPDLETRLAILQKKAEEEG--LE  287 (405)
T ss_pred             hhcCCHHHHHHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhhhccCCeEEEeCCCCHHHHHHHHHHHHHHcC--CC
Confidence            432   11 222222211 123456888876422         112223345788999999999999988774322  12


Q ss_pred             cHHHHHHHHHHHhCCCchH
Q 039644          145 GYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       145 ~~~~~~~~i~~~~~g~Pla  163 (192)
                      -.++...-|++.+.|.+-.
T Consensus       288 l~~e~l~~ia~~~~~~~r~  306 (405)
T TIGR00362       288 LPDEVLEFIAKNIRSNVRE  306 (405)
T ss_pred             CCHHHHHHHHHhcCCCHHH
Confidence            2244555666666665543

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).

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.80  E-value=0.0014  Score=54.90  Aligned_cols=94  Identities=14%  Similarity=0.104  Sum_probs=58.7

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhh-cCCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRN-WGVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~-~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +++-++|+|+++...  .++.+...+.+....+.+|++|.+.. +... .+....+++++++.++....+...+-...  
T Consensus       118 g~~kViIIDEa~~ls~~a~naLLK~LEepp~~v~fIL~Ttd~~kil~tI~SRc~~~~f~~Ls~~eI~~~L~~il~~eg--  195 (546)
T PRK14957        118 GRYKVYLIDEVHMLSKQSFNALLKTLEEPPEYVKFILATTDYHKIPVTILSRCIQLHLKHISQADIKDQLKIILAKEN--  195 (546)
T ss_pred             CCcEEEEEechhhccHHHHHHHHHHHhcCCCCceEEEEECChhhhhhhHHHheeeEEeCCCCHHHHHHHHHHHHHHcC--
Confidence            456699999998553  46777766665555666666554432 2222 24467899999999998877776442211  


Q ss_pred             CccHHHHHHHHHHHhCCCch
Q 039644          143 DVGYEKLSSNVTKYAQGIPL  162 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Pl  162 (192)
                      -.........|++.++|.+.
T Consensus       196 i~~e~~Al~~Ia~~s~GdlR  215 (546)
T PRK14957        196 INSDEQSLEYIAYHAKGSLR  215 (546)
T ss_pred             CCCCHHHHHHHHHHcCCCHH
Confidence            12234445567777777654

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.80  E-value=0.0004  Score=57.14  Aligned_cols=144  Identities=10%  Similarity=0.137  Sum_probs=81.7

Q ss_pred             CchhHHHHHHHHHhhCCCcc--eEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCC
Q 039644            1 IGKTAIARAIFDKISGDFEC--SCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVT   78 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~--~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~   78 (192)
                      +|||+|++.+++.+.++++.  ++++.           ..++...+...+...     ....+...++. .-+|+|||++
T Consensus       159 ~GKThL~~ai~~~~~~~~~~~~v~yi~-----------~~~~~~~~~~~~~~~-----~~~~~~~~~~~-~dlLiiDDi~  221 (450)
T PRK00149        159 LGKTHLLHAIGNYILEKNPNAKVVYVT-----------SEKFTNDFVNALRNN-----TMEEFKEKYRS-VDVLLIDDIQ  221 (450)
T ss_pred             CCHHHHHHHHHHHHHHhCCCCeEEEEE-----------HHHHHHHHHHHHHcC-----cHHHHHHHHhc-CCEEEEehhh
Confidence            69999999999988776543  33443           344444554444321     22334444443 3489999997


Q ss_pred             Cch----hHHHhhccCCC-CCCCceEEEEecchh---------HHhhcCCCceEecCCCCHHHHHHHHHHhhcCCCCCCc
Q 039644           79 CFS----QLESLMGSLDW-LTPVSRIILTTRNKQ---------VLRNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDV  144 (192)
Q Consensus        79 ~~~----~~~~l~~~~~~-~~~~~~iivTtR~~~---------~~~~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~  144 (192)
                      ...    ..+.+...+.. ...+..+|+||....         +...+.....+.+++.+.++-..++...+-...  -.
T Consensus       222 ~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~l~SRl~~gl~v~i~~pd~~~r~~il~~~~~~~~--~~  299 (450)
T PRK00149        222 FLAGKERTQEEFFHTFNALHEAGKQIVLTSDRPPKELPGLEERLRSRFEWGLTVDIEPPDLETRIAILKKKAEEEG--ID  299 (450)
T ss_pred             hhcCCHHHHHHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHhHhcCCeeEEecCCCHHHHHHHHHHHHHHcC--CC
Confidence            421    11222221111 123455888876532         122223456789999999999999998774322  12


Q ss_pred             cHHHHHHHHHHHhCCCchH
Q 039644          145 GYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       145 ~~~~~~~~i~~~~~g~Pla  163 (192)
                      -.++...-|++.+.|....
T Consensus       300 l~~e~l~~ia~~~~~~~R~  318 (450)
T PRK00149        300 LPDEVLEFIAKNITSNVRE  318 (450)
T ss_pred             CCHHHHHHHHcCcCCCHHH
Confidence            2334455566666665543

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.78  E-value=0.0015  Score=54.04  Aligned_cols=95  Identities=16%  Similarity=0.189  Sum_probs=61.4

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecch-hHHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNK-QVLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~-~~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      ++.-++|+|+++...  .++.+...+.+....+++|++|.+. .+.... +....+.+.+++.++....+...+....  
T Consensus       115 ~~~KVvIIDEah~Ls~~A~NaLLK~LEePp~~v~fIlatte~~Kl~~tI~SRc~~~~f~~l~~~el~~~L~~ia~~Eg--  192 (491)
T PRK14964        115 SKFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKFILATTEVKKIPVTIISRCQRFDLQKIPTDKLVEHLVDIAKKEN--  192 (491)
T ss_pred             CCceEEEEeChHhCCHHHHHHHHHHHhCCCCCeEEEEEeCChHHHHHHHHHhheeeecccccHHHHHHHHHHHHHHcC--
Confidence            345589999998553  4677777666655667777766442 332222 4567899999999998888887664322  


Q ss_pred             CccHHHHHHHHHHHhCCCchH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Pla  163 (192)
                      -.-.++....|++.++|.+..
T Consensus       193 i~i~~eAL~lIa~~s~GslR~  213 (491)
T PRK14964        193 IEHDEESLKLIAENSSGSMRN  213 (491)
T ss_pred             CCCCHHHHHHHHHHcCCCHHH
Confidence            122334455677777777653

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=97.77  E-value=0.0018  Score=52.36  Aligned_cols=91  Identities=11%  Similarity=0.109  Sum_probs=59.3

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +++-++++|+++...  ..+.+...+.....++.+|++|.+.. +...+ +....+.+.+++.++..+.+....+   . 
T Consensus       116 ~~~kViiIDead~m~~~aanaLLk~LEep~~~~~fIL~a~~~~~llpTIrSRc~~i~f~~~~~~~i~~~L~~~~~---~-  191 (394)
T PRK07940        116 GRWRIVVIEDADRLTERAANALLKAVEEPPPRTVWLLCAPSPEDVLPTIRSRCRHVALRTPSVEAVAEVLVRRDG---V-  191 (394)
T ss_pred             CCcEEEEEechhhcCHHHHHHHHHHhhcCCCCCeEEEEECChHHChHHHHhhCeEEECCCCCHHHHHHHHHHhcC---C-
Confidence            445588899998664  34555555555455676777776643 22222 4467899999999999888864321   1 


Q ss_pred             CccHHHHHHHHHHHhCCCchHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLAL  164 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai  164 (192)
                         ..+.+..++..++|.|...
T Consensus       192 ---~~~~a~~la~~s~G~~~~A  210 (394)
T PRK07940        192 ---DPETARRAARASQGHIGRA  210 (394)
T ss_pred             ---CHHHHHHHHHHcCCCHHHH
Confidence               1344567788888988644

>PLN03025 replication factor C subunit; Provisional

Probab=97.77  E-value=0.00092  Score=52.52  Aligned_cols=147  Identities=11%  Similarity=0.122  Sum_probs=78.0

Q ss_pred             CchhHHHHHHHHHh-hCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKI-SGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~-~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~   79 (192)
                      +||||+|..+++.+ ...|...+.-.+.++.    ... +..+...+.+......         ...++.-+++||+++.
T Consensus        45 ~GKTtla~~la~~l~~~~~~~~~~eln~sd~----~~~-~~vr~~i~~~~~~~~~---------~~~~~~kviiiDE~d~  110 (319)
T PLN03025         45 TGKTTSILALAHELLGPNYKEAVLELNASDD----RGI-DVVRNKIKMFAQKKVT---------LPPGRHKIVILDEADS  110 (319)
T ss_pred             CCHHHHHHHHHHHHhcccCccceeeeccccc----ccH-HHHHHHHHHHHhcccc---------CCCCCeEEEEEechhh
Confidence            69999999999975 3334322111111110    122 2233333322211100         0023466999999986


Q ss_pred             chh--HHHhhccCCCCCCCceEEEEecchhHH-hh-cCCCceEecCCCCHHHHHHHHHHhhcCCCCCCccHHHHHHHHHH
Q 039644           80 FSQ--LESLMGSLDWLTPVSRIILTTRNKQVL-RN-WGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTK  155 (192)
Q Consensus        80 ~~~--~~~l~~~~~~~~~~~~iivTtR~~~~~-~~-~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~  155 (192)
                      ...  ...+...+......+++++++...... .. -+....+++++++.++....+...+-....  .-.++....+++
T Consensus       111 lt~~aq~aL~~~lE~~~~~t~~il~~n~~~~i~~~L~SRc~~i~f~~l~~~~l~~~L~~i~~~egi--~i~~~~l~~i~~  188 (319)
T PLN03025        111 MTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAEKV--PYVPEGLEAIIF  188 (319)
T ss_pred             cCHHHHHHHHHHHhcccCCceEEEEeCCccccchhHHHhhhcccCCCCCHHHHHHHHHHHHHHcCC--CCCHHHHHHHHH
Confidence            642  344443343334567777777543211 11 133467999999999988888776532221  112344566777


Q ss_pred             HhCCCchH
Q 039644          156 YAQGIPLA  163 (192)
Q Consensus       156 ~~~g~Pla  163 (192)
                      .++|....
T Consensus       189 ~~~gDlR~  196 (319)
T PLN03025        189 TADGDMRQ  196 (319)
T ss_pred             HcCCCHHH
Confidence            77776543

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.77  E-value=0.0015  Score=55.54  Aligned_cols=95  Identities=13%  Similarity=0.149  Sum_probs=60.3

Q ss_pred             ceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecch-hHHhh-cCCCceEecCCCCHHHHHHHHHHhhcCCCCCC
Q 039644           68 MKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNK-QVLRN-WGVSKIYEMEALEYHHALELFSQHAFKRNHPD  143 (192)
Q Consensus        68 ~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~-~~~~~-~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~  143 (192)
                      +.-++|||+++...  .++.+...+......+++|++|.+. .+... .+....+.+++++.++....+...+.....  
T Consensus       124 ~~KV~IIDEvh~Ls~~a~NaLLKtLEEPP~~~~fIL~Ttd~~kil~TIlSRc~~~~f~~Ls~eei~~~L~~i~~~egi--  201 (618)
T PRK14951        124 RFKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATTDPQKVPVTVLSRCLQFNLRPMAPETVLEHLTQVLAAENV--  201 (618)
T ss_pred             CceEEEEEChhhCCHHHHHHHHHhcccCCCCeEEEEEECCchhhhHHHHHhceeeecCCCCHHHHHHHHHHHHHHcCC--
Confidence            34489999999654  4777777666555666777666442 22212 245678999999999988888776532221  


Q ss_pred             ccHHHHHHHHHHHhCCCchHH
Q 039644          144 VGYEKLSSNVTKYAQGIPLAL  164 (192)
Q Consensus       144 ~~~~~~~~~i~~~~~g~Plai  164 (192)
                      ....+....|++.++|.+.-+
T Consensus       202 ~ie~~AL~~La~~s~GslR~a  222 (618)
T PRK14951        202 PAEPQALRLLARAARGSMRDA  222 (618)
T ss_pred             CCCHHHHHHHHHHcCCCHHHH
Confidence            122344566777777766443

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.75  E-value=0.00093  Score=55.74  Aligned_cols=96  Identities=11%  Similarity=0.061  Sum_probs=58.5

Q ss_pred             CceEEEEEeCCCCc--hhHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCF--SQLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      ++.-++|+|+++..  ..++.+...+......+++|++|.+.. +.... +....+++++++.++....+...+-.... 
T Consensus       118 ~~~kV~iIDE~~~ls~~a~naLLk~LEepp~~~~fIlattd~~kl~~tI~SRc~~~~f~~l~~~~i~~~l~~il~~egi-  196 (509)
T PRK14958        118 GRFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVKFILATTDHHKLPVTVLSRCLQFHLAQLPPLQIAAHCQHLLKEENV-  196 (509)
T ss_pred             CCcEEEEEEChHhcCHHHHHHHHHHHhccCCCeEEEEEECChHhchHHHHHHhhhhhcCCCCHHHHHHHHHHHHHHcCC-
Confidence            44558999999865  346767666665556677777665432 21111 34567889999998877766555422211 


Q ss_pred             CccHHHHHHHHHHHhCCCchHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLAL  164 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai  164 (192)
                       .........|++.++|.+..+
T Consensus       197 -~~~~~al~~ia~~s~GslR~a  217 (509)
T PRK14958        197 -EFENAALDLLARAANGSVRDA  217 (509)
T ss_pred             -CCCHHHHHHHHHHcCCcHHHH
Confidence             112344556777777776543

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=97.75  E-value=0.0016  Score=51.26  Aligned_cols=95  Identities=13%  Similarity=0.054  Sum_probs=57.1

Q ss_pred             ceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchhH-Hhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCCC
Q 039644           68 MKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQV-LRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHPD  143 (192)
Q Consensus        68 ~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~~-~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~  143 (192)
                      .+-++|+||++...  ....+...+......+++|+|+..... .... +....+.+.+++.++....+...+.....  
T Consensus       125 ~~~vlilDe~~~l~~~~~~~L~~~le~~~~~~~~Il~~~~~~~~~~~L~sr~~~v~~~~~~~~~~~~~l~~~~~~~~~--  202 (337)
T PRK12402        125 DYKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIPPIRSRCLPLFFRAPTDDELVDVLESIAEAEGV--  202 (337)
T ss_pred             CCcEEEEeCcccCCHHHHHHHHHHHHhccCCCeEEEEeCChhhCchhhcCCceEEEecCCCHHHHHHHHHHHHHHcCC--
Confidence            44589999998653  234444433333455778888754321 1111 34567889999999988888776532221  


Q ss_pred             ccHHHHHHHHHHHhCCCchHH
Q 039644          144 VGYEKLSSNVTKYAQGIPLAL  164 (192)
Q Consensus       144 ~~~~~~~~~i~~~~~g~Plai  164 (192)
                      .-..+....+++.++|.+-.+
T Consensus       203 ~~~~~al~~l~~~~~gdlr~l  223 (337)
T PRK12402        203 DYDDDGLELIAYYAGGDLRKA  223 (337)
T ss_pred             CCCHHHHHHHHHHcCCCHHHH
Confidence            123445666777777765543

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.74  E-value=0.0013  Score=53.98  Aligned_cols=142  Identities=10%  Similarity=0.119  Sum_probs=79.0

Q ss_pred             CchhHHHHHHHHHhhCCCcc--eEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCC
Q 039644            1 IGKTAIARAIFDKISGDFEC--SCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVT   78 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~--~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~   78 (192)
                      +|||+|+..+++.+.+.++.  ++|+.           ..++...+...+...     ....++..++...-+|+|||++
T Consensus       141 ~GKTHLl~ai~~~l~~~~~~~~v~yi~-----------~~~f~~~~~~~~~~~-----~~~~f~~~~~~~~dvLlIDDi~  204 (440)
T PRK14088        141 LGKTHLLQSIGNYVVQNEPDLRVMYIT-----------SEKFLNDLVDSMKEG-----KLNEFREKYRKKVDVLLIDDVQ  204 (440)
T ss_pred             CcHHHHHHHHHHHHHHhCCCCeEEEEE-----------HHHHHHHHHHHHhcc-----cHHHHHHHHHhcCCEEEEechh
Confidence            69999999999987665432  34443           345555555554322     2233444444455689999997


Q ss_pred             Cch---hH-HHhhccCCC-CCCCceEEEEecc-hhH--------HhhcCCCceEecCCCCHHHHHHHHHHhhcCCCCCCc
Q 039644           79 CFS---QL-ESLMGSLDW-LTPVSRIILTTRN-KQV--------LRNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDV  144 (192)
Q Consensus        79 ~~~---~~-~~l~~~~~~-~~~~~~iivTtR~-~~~--------~~~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~  144 (192)
                      ...   .+ +.+...+.. ...+..+|+||.. +.-        ...+..+..+.+++.+.+.-..++.+.+.....  .
T Consensus       205 ~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~rL~SR~~~gl~v~i~~pd~e~r~~IL~~~~~~~~~--~  282 (440)
T PRK14088        205 FLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKKIARKMLEIEHG--E  282 (440)
T ss_pred             hhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHHHHhhHHhcCceEeeCCCCHHHHHHHHHHHHHhcCC--C
Confidence            431   11 222222111 1234568888753 221        111233457889999999999998887643221  1


Q ss_pred             cHHHHHHHHHHHhCCC
Q 039644          145 GYEKLSSNVTKYAQGI  160 (192)
Q Consensus       145 ~~~~~~~~i~~~~~g~  160 (192)
                      -.++...-|++.+.|.
T Consensus       283 l~~ev~~~Ia~~~~~~  298 (440)
T PRK14088        283 LPEEVLNFVAENVDDN  298 (440)
T ss_pred             CCHHHHHHHHhccccC
Confidence            2234445555555544

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=97.73  E-value=6.2e-05  Score=60.02  Aligned_cols=77  Identities=18%  Similarity=0.245  Sum_probs=50.4

Q ss_pred             CchhHHHHHHHHHhhC-CCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC--cC--------chHHHHhh-cCCc
Q 039644            1 IGKTAIARAIFDKISG-DFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV--MP--------YIDLNFRR-LSRM   68 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~-~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--~~--------~~~~l~~~-l~~~   68 (192)
                      +||||||+++++.+.. +|+..+|+.++++.   +..+.+++..+...+.....+  ..        ..+..... -.++
T Consensus       180 vGKTTLaK~Ian~I~~nhFDv~~~VvLIgER---~~EVtdiqrsIlg~vv~st~d~~~~~~~~~a~~~ie~Ae~~~e~G~  256 (416)
T PRK09376        180 AGKTVLLQNIANSITTNHPEVHLIVLLIDER---PEEVTDMQRSVKGEVVASTFDEPAERHVQVAEMVIEKAKRLVEHGK  256 (416)
T ss_pred             CChhHHHHHHHHHHHhhcCCeEEEEEEeCCc---hhHHHHHHHHhcCcEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence            6999999999997643 79999999876552   136778887776433222222  11        22222222 2578


Q ss_pred             eEEEEEeCCCCc
Q 039644           69 KVLIVFDDVTCF   80 (192)
Q Consensus        69 ~~LlVlDdv~~~   80 (192)
                      +.||++|++...
T Consensus       257 dVlL~iDsItR~  268 (416)
T PRK09376        257 DVVILLDSITRL  268 (416)
T ss_pred             CEEEEEEChHHH
Confidence            999999999643

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=97.72  E-value=0.0072  Score=48.14  Aligned_cols=98  Identities=9%  Similarity=0.123  Sum_probs=63.2

Q ss_pred             CceEEEEEeCCCCchh--HHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFSQ--LESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~~--~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      ++.-++|+|+++....  .+.+...+.....++.+|++|.... +.... +....+.+.+++.++..+.+......  . 
T Consensus       140 g~~rVviIDeAd~l~~~aanaLLk~LEEpp~~~~fiLit~~~~~llptIrSRc~~i~l~pl~~~~~~~~L~~~~~~--~-  216 (351)
T PRK09112        140 GNWRIVIIDPADDMNRNAANAILKTLEEPPARALFILISHSSGRLLPTIRSRCQPISLKPLDDDELKKALSHLGSS--Q-  216 (351)
T ss_pred             CCceEEEEEchhhcCHHHHHHHHHHHhcCCCCceEEEEECChhhccHHHHhhccEEEecCCCHHHHHHHHHHhhcc--c-
Confidence            4566999999996643  5555555554445566666665443 22222 34578999999999999998874311  1 


Q ss_pred             CccHHHHHHHHHHHhCCCchHHHHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLALKVLS  168 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai~~~~  168 (192)
                      . ...+....+++.++|.|.....+.
T Consensus       217 ~-~~~~~~~~i~~~s~G~pr~Al~ll  241 (351)
T PRK09112        217 G-SDGEITEALLQRSKGSVRKALLLL  241 (351)
T ss_pred             C-CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            1 223446788999999998654443

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.71  E-value=0.0017  Score=57.05  Aligned_cols=94  Identities=9%  Similarity=0.065  Sum_probs=59.6

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      ++.-++|||+++...  .++.|...+.+....+.+|++|.+.+ +...+ +....+.+..++.++..+.+.+.+-...  
T Consensus       119 ~~~KV~IIDEad~lt~~a~NaLLK~LEEpP~~~~fIl~tt~~~kLl~TIrSRc~~v~F~~l~~~~l~~~L~~il~~EG--  196 (824)
T PRK07764        119 SRYKIFIIDEAHMVTPQGFNALLKIVEEPPEHLKFIFATTEPDKVIGTIRSRTHHYPFRLVPPEVMRGYLERICAQEG--  196 (824)
T ss_pred             CCceEEEEechhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhHHHHhheeEEEeeCCCHHHHHHHHHHHHHHcC--
Confidence            455589999999664  46777777766666777776664433 33222 4567899999999988887776542211  


Q ss_pred             CccHHHHHHHHHHHhCCCch
Q 039644          143 DVGYEKLSSNVTKYAQGIPL  162 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Pl  162 (192)
                      ..........|++.++|.+.
T Consensus       197 v~id~eal~lLa~~sgGdlR  216 (824)
T PRK07764        197 VPVEPGVLPLVIRAGGGSVR  216 (824)
T ss_pred             CCCCHHHHHHHHHHcCCCHH
Confidence            11123344566777777663

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.64  E-value=0.001  Score=56.94  Aligned_cols=98  Identities=10%  Similarity=0.070  Sum_probs=60.7

Q ss_pred             CceEEEEEeCCCCchh--HHHhhccCCCCCCCceEEEEecchh-HHhh-cCCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFSQ--LESLMGSLDWLTPVSRIILTTRNKQ-VLRN-WGVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~~--~~~l~~~~~~~~~~~~iivTtR~~~-~~~~-~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      ++.-++|||+++....  .+.+...+......+++|++|.+.. +... .+....+.+.+++.++....+...+-...  
T Consensus       118 gk~KVIIIDEad~Ls~~A~NALLKtLEEPp~~v~fILaTtd~~kL~~TIrSRC~~f~f~~Ls~eeI~~~L~~Il~kEg--  195 (709)
T PRK08691        118 GKYKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPHKVPVTVLSRCLQFVLRNMTAQQVADHLAHVLDSEK--  195 (709)
T ss_pred             CCcEEEEEECccccCHHHHHHHHHHHHhCCCCcEEEEEeCCccccchHHHHHHhhhhcCCCCHHHHHHHHHHHHHHcC--
Confidence            4556899999986543  5556655544445667777775432 1111 13345688889999998888877653222  


Q ss_pred             CccHHHHHHHHHHHhCCCchHHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLALKV  166 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai~~  166 (192)
                      -.........|++.++|.+.-+..
T Consensus       196 i~id~eAL~~Ia~~A~GslRdAln  219 (709)
T PRK08691        196 IAYEPPALQLLGRAAAGSMRDALS  219 (709)
T ss_pred             CCcCHHHHHHHHHHhCCCHHHHHH
Confidence            122344566788888888754433

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=97.63  E-value=0.0028  Score=53.66  Aligned_cols=121  Identities=15%  Similarity=0.244  Sum_probs=71.1

Q ss_pred             CchhHHHHHHHHHhhCCCc--ceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCC
Q 039644            1 IGKTAIARAIFDKISGDFE--CSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVT   78 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~--~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~   78 (192)
                      +|||.|+..+++.+...+.  .++++.           ..++...+...+...     ....+++.+.+- =+|||||+.
T Consensus       325 sGKTHLL~AIa~~a~~~~~g~~V~Yit-----------aeef~~el~~al~~~-----~~~~f~~~y~~~-DLLlIDDIq  387 (617)
T PRK14086        325 LGKTHLLHAIGHYARRLYPGTRVRYVS-----------SEEFTNEFINSIRDG-----KGDSFRRRYREM-DILLVDDIQ  387 (617)
T ss_pred             CCHHHHHHHHHHHHHHhCCCCeEEEee-----------HHHHHHHHHHHHHhc-----cHHHHHHHhhcC-CEEEEehhc
Confidence            6999999999998765443  234443           444554544443321     223344444432 478899997


Q ss_pred             Cch---hH-HHhhccCCC-CCCCceEEEEecch---------hHHhhcCCCceEecCCCCHHHHHHHHHHhhcC
Q 039644           79 CFS---QL-ESLMGSLDW-LTPVSRIILTTRNK---------QVLRNWGVSKIYEMEALEYHHALELFSQHAFK  138 (192)
Q Consensus        79 ~~~---~~-~~l~~~~~~-~~~~~~iivTtR~~---------~~~~~~~~~~~~~l~~l~~~ea~~lf~~~~~~  138 (192)
                      ...   .| +.|...+.. ...+..||+||...         .+...+...-.+.++..+.+.-.+++.+.+-.
T Consensus       388 ~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~SRf~~GLvv~I~~PD~EtR~aIL~kka~~  461 (617)
T PRK14086        388 FLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRNRFEWGLITDVQPPELETRIAILRKKAVQ  461 (617)
T ss_pred             cccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHhhhhcCceEEcCCCCHHHHHHHHHHHHHh
Confidence            431   12 222222211 12356688888753         23333345678899999999999999887643

>PRK04195 replication factor C large subunit; Provisional

Probab=97.63  E-value=0.0019  Score=53.69  Aligned_cols=141  Identities=14%  Similarity=0.186  Sum_probs=76.6

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +||||+|+.+++++.  |+. +-+. .++     ....+.+..++.......+          .+...+-+||||+++..
T Consensus        50 ~GKTtla~ala~el~--~~~-ieln-asd-----~r~~~~i~~~i~~~~~~~s----------l~~~~~kvIiIDEaD~L  110 (482)
T PRK04195         50 VGKTSLAHALANDYG--WEV-IELN-ASD-----QRTADVIERVAGEAATSGS----------LFGARRKLILLDEVDGI  110 (482)
T ss_pred             CCHHHHHHHHHHHcC--CCE-EEEc-ccc-----cccHHHHHHHHHHhhccCc----------ccCCCCeEEEEecCccc
Confidence            699999999999873  222 1121 222     1222233333333222111          11135779999999864


Q ss_pred             hh------HHHhhccCCCCCCCceEEEEecchhHHh--h-cCCCceEecCCCCHHHHHHHHHHhhcCCCCCCccHHHHHH
Q 039644           81 SQ------LESLMGSLDWLTPVSRIILTTRNKQVLR--N-WGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSS  151 (192)
Q Consensus        81 ~~------~~~l~~~~~~~~~~~~iivTtR~~~~~~--~-~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~~  151 (192)
                      ..      +..+...+.  ..+..+|+++....-..  . -.....+.+.+++..+....+...+.....  ....+...
T Consensus       111 ~~~~d~~~~~aL~~~l~--~~~~~iIli~n~~~~~~~k~Lrsr~~~I~f~~~~~~~i~~~L~~i~~~egi--~i~~eaL~  186 (482)
T PRK04195        111 HGNEDRGGARAILELIK--KAKQPIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGI--ECDDEALK  186 (482)
T ss_pred             ccccchhHHHHHHHHHH--cCCCCEEEeccCccccchhhHhccceEEEecCCCHHHHHHHHHHHHHHcCC--CCCHHHHH
Confidence            32      445544433  23345777764432111  1 134567899999999988888776533221  11234566


Q ss_pred             HHHHHhCCCchHH
Q 039644          152 NVTKYAQGIPLAL  164 (192)
Q Consensus       152 ~i~~~~~g~Plai  164 (192)
                      .|++.++|....+
T Consensus       187 ~Ia~~s~GDlR~a  199 (482)
T PRK04195        187 EIAERSGGDLRSA  199 (482)
T ss_pred             HHHHHcCCCHHHH
Confidence            6777777665543

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.63  E-value=0.0037  Score=48.85  Aligned_cols=94  Identities=11%  Similarity=0.120  Sum_probs=57.9

Q ss_pred             ceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhh-cCCCceEecCCCCHHHHHHHHHHhhcCCCCCC
Q 039644           68 MKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRN-WGVSKIYEMEALEYHHALELFSQHAFKRNHPD  143 (192)
Q Consensus        68 ~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~-~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~  143 (192)
                      .+-++++|+++...  ....+...+......+++|+++.... .... ......+.+++++.++....+...+.....  
T Consensus       102 ~~~vviiDe~~~l~~~~~~~L~~~le~~~~~~~lIl~~~~~~~l~~~l~sr~~~~~~~~l~~~ei~~~l~~~~~~~~~--  179 (319)
T PRK00440        102 PFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSRCAVFRFSPLKKEAVAERLRYIAENEGI--  179 (319)
T ss_pred             CceEEEEeCcccCCHHHHHHHHHHHhcCCCCCeEEEEeCCccccchhHHHHhheeeeCCCCHHHHHHHHHHHHHHcCC--
Confidence            35689999997553  24455544444445567777764322 1111 123457899999999988888876643221  


Q ss_pred             ccHHHHHHHHHHHhCCCchH
Q 039644          144 VGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       144 ~~~~~~~~~i~~~~~g~Pla  163 (192)
                      .-..+....+++.++|.+.-
T Consensus       180 ~i~~~al~~l~~~~~gd~r~  199 (319)
T PRK00440        180 EITDDALEAIYYVSEGDMRK  199 (319)
T ss_pred             CCCHHHHHHHHHHcCCCHHH
Confidence            12345566778888887665

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.61  E-value=0.0019  Score=54.18  Aligned_cols=94  Identities=12%  Similarity=0.082  Sum_probs=59.3

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhh-cCCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRN-WGVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~-~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +++-++|+|+++...  ..+.+...+......+.+|++|.+.. +... .+....+++++++.++....+...+....  
T Consensus       118 ~~~kVvIIDEad~ls~~a~naLLK~LEepp~~~~fIL~t~d~~kil~tI~SRc~~~~f~~l~~~~i~~~L~~il~~eg--  195 (527)
T PRK14969        118 GRFKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPPLIVSHLQHILEQEN--  195 (527)
T ss_pred             CCceEEEEcCcccCCHHHHHHHHHHHhCCCCCEEEEEEeCChhhCchhHHHHHHHHhcCCCCHHHHHHHHHHHHHHcC--
Confidence            456699999998654  36667666665555666777664432 1111 12346788999999998877766543211  


Q ss_pred             CccHHHHHHHHHHHhCCCch
Q 039644          143 DVGYEKLSSNVTKYAQGIPL  162 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Pl  162 (192)
                      -.........|++.++|.+.
T Consensus       196 i~~~~~al~~la~~s~Gslr  215 (527)
T PRK14969        196 IPFDATALQLLARAAAGSMR  215 (527)
T ss_pred             CCCCHHHHHHHHHHcCCCHH
Confidence            11223445677888888775

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

Probab=97.59  E-value=0.0032  Score=50.74  Aligned_cols=121  Identities=14%  Similarity=0.179  Sum_probs=76.4

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||.|+..+++...++.+....+.         ....++...++..+..+     ....+++..  .-=++++||++-.
T Consensus       124 lGKTHLl~Aign~~~~~~~~a~v~y---------~~se~f~~~~v~a~~~~-----~~~~Fk~~y--~~dlllIDDiq~l  187 (408)
T COG0593         124 LGKTHLLQAIGNEALANGPNARVVY---------LTSEDFTNDFVKALRDN-----EMEKFKEKY--SLDLLLIDDIQFL  187 (408)
T ss_pred             CCHHHHHHHHHHHHHhhCCCceEEe---------ccHHHHHHHHHHHHHhh-----hHHHHHHhh--ccCeeeechHhHh
Confidence            5999999999998877776444443         24556666666655443     334455555  3338899999742


Q ss_pred             h---hH-HHhhccCCC-CCCCceEEEEecch---------hHHhhcCCCceEecCCCCHHHHHHHHHHhhc
Q 039644           81 S---QL-ESLMGSLDW-LTPVSRIILTTRNK---------QVLRNWGVSKIYEMEALEYHHALELFSQHAF  137 (192)
Q Consensus        81 ~---~~-~~l~~~~~~-~~~~~~iivTtR~~---------~~~~~~~~~~~~~l~~l~~~ea~~lf~~~~~  137 (192)
                      .   .+ +.+...+.. ...|..||+|++..         ...+.+..+-.+.+.+.+.+....++.+.+-
T Consensus       188 ~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~SR~~~Gl~~~I~~Pd~e~r~aiL~kka~  258 (408)
T COG0593         188 AGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIEPPDDETRLAILRKKAE  258 (408)
T ss_pred             cCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHHHHHhceeEEeeCCCCHHHHHHHHHHHHH
Confidence            1   11 222222211 12344799998542         3334445567899999999999999988654

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=97.58  E-value=0.0014  Score=52.45  Aligned_cols=138  Identities=20%  Similarity=0.286  Sum_probs=74.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhc-CCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRL-SRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l-~~~~~LlVlDdv~~   79 (192)
                      +|||++|+.+++.....|-.+     .         ..++.....    +..  ......+.... ...+.+|+||+++.
T Consensus       167 tGKT~lakaia~~l~~~~~~v-----~---------~~~l~~~~~----g~~--~~~i~~~f~~a~~~~p~il~iDEiD~  226 (364)
T TIGR01242       167 TGKTLLAKAVAHETNATFIRV-----V---------GSELVRKYI----GEG--ARLVREIFELAKEKAPSIIFIDEIDA  226 (364)
T ss_pred             CCHHHHHHHHHHhCCCCEEec-----c---------hHHHHHHhh----hHH--HHHHHHHHHHHHhcCCcEEEhhhhhh
Confidence            699999999999876554221     1         111111100    000  00112222222 34678999999974


Q ss_pred             ch----------------hHHHhhccCCC--CCCCceEEEEecchhHHhhc-----CCCceEecCCCCHHHHHHHHHHhh
Q 039644           80 FS----------------QLESLMGSLDW--LTPVSRIILTTRNKQVLRNW-----GVSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus        80 ~~----------------~~~~l~~~~~~--~~~~~~iivTtR~~~~~~~~-----~~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      ..                .+..+...+..  ...+..||.||+........     .....+.++..+.++..++|..+.
T Consensus       227 l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~~~~~~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~  306 (364)
T TIGR01242       227 IAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHT  306 (364)
T ss_pred             hccccccCCCCccHHHHHHHHHHHHHhhCCCCCCCEEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHHHHHHHHHH
Confidence            31                12233322222  12456788888754322111     224578899999999999998876


Q ss_pred             cCCCCCC-ccHHHHHHHHHHHhCCCch
Q 039644          137 FKRNHPD-VGYEKLSSNVTKYAQGIPL  162 (192)
Q Consensus       137 ~~~~~~~-~~~~~~~~~i~~~~~g~Pl  162 (192)
                      ....... ..    ...+++.+.|..-
T Consensus       307 ~~~~l~~~~~----~~~la~~t~g~sg  329 (364)
T TIGR01242       307 RKMKLAEDVD----LEAIAKMTEGASG  329 (364)
T ss_pred             hcCCCCccCC----HHHHHHHcCCCCH
Confidence            4433221 22    3466777777653

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=97.57  E-value=0.00018  Score=54.36  Aligned_cols=77  Identities=17%  Similarity=0.246  Sum_probs=49.8

Q ss_pred             CchhHHHHHHHHHhh-CCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC----c--C----chHHHHhh-cCCc
Q 039644            1 IGKTAIARAIFDKIS-GDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV----M--P----YIDLNFRR-LSRM   68 (192)
Q Consensus         1 iGKTtLa~~~~~~~~-~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~----~--~----~~~~l~~~-l~~~   68 (192)
                      +|||||++.+++.+. .+|+..+|+.++.+.   +..+.+++..+...+.-...+    .  .    ........ -.++
T Consensus        27 ~GKTTLlr~I~n~l~~~~fdv~~~v~vI~er---~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~~~~a~~~~~~G~  103 (249)
T cd01128          27 AGKTTLLQSIANAITKNHPEVYLIVLLIDER---PEEVTDMQRSVKGEVIASTFDEPPERHVQVAEMVLEKAKRLVEHGK  103 (249)
T ss_pred             CCHHHHHHHHHhccccccCCeEEEEEEccCC---CccHHHHHHHhccEEEEecCCCCHHHHHHHHHHHHHHHHHHHHCCC
Confidence            699999999999754 479999999855431   257888888883333222111    1  1    22222222 2478


Q ss_pred             eEEEEEeCCCCc
Q 039644           69 KVLIVFDDVTCF   80 (192)
Q Consensus        69 ~~LlVlDdv~~~   80 (192)
                      +.++++|++...
T Consensus       104 ~vll~iDei~r~  115 (249)
T cd01128         104 DVVILLDSITRL  115 (249)
T ss_pred             CEEEEEECHHHh
Confidence            999999999644

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.

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.54  E-value=0.003  Score=52.03  Aligned_cols=95  Identities=11%  Similarity=0.054  Sum_probs=59.9

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecc-hhHHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRN-KQVLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~-~~~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      ++.-++|+|+++...  .++.+...+........+|.+|.. ..+...+ +....+.+.+++.++..+.+...+....  
T Consensus       120 g~~KV~IIDEah~Ls~~A~NALLKtLEEPp~~viFILaTte~~kI~~TI~SRCq~~~f~~ls~~~i~~~L~~i~~~Eg--  197 (484)
T PRK14956        120 GKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKIPETILSRCQDFIFKKVPLSVLQDYSEKLCKIEN--  197 (484)
T ss_pred             CCCEEEEEechhhcCHHHHHHHHHHhhcCCCceEEEeecCChhhccHHHHhhhheeeecCCCHHHHHHHHHHHHHHcC--
Confidence            455699999998654  477777666554445555555544 3222222 4456799999999998888877653222  


Q ss_pred             CccHHHHHHHHHHHhCCCchH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Pla  163 (192)
                      -.-..+....|++.++|.+.-
T Consensus       198 i~~e~eAL~~Ia~~S~Gd~Rd  218 (484)
T PRK14956        198 VQYDQEGLFWIAKKGDGSVRD  218 (484)
T ss_pred             CCCCHHHHHHHHHHcCChHHH
Confidence            122344556677777777644

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=97.53  E-value=0.012  Score=46.72  Aligned_cols=99  Identities=13%  Similarity=0.112  Sum_probs=62.3

Q ss_pred             CceEEEEEeCCCCc--hhHHHhhccCCCCCCCceEEEEecchhH-Hhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCF--SQLESLMGSLDWLTPVSRIILTTRNKQV-LRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~iivTtR~~~~-~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +.+-++|+|+++..  ...+.+...+......+.+|++|.+... .... +....+++.+++.++..+.+...+-.... 
T Consensus       116 ~~~~vviidea~~l~~~~~~~Ll~~le~~~~~~~lIl~~~~~~~l~~~l~sr~~~~~~~~~~~~~l~~~l~~~~~~~g~-  194 (355)
T TIGR02397       116 GKYKVYIIDEVHMLSKSAFNALLKTLEEPPEHVVFILATTEPHKIPATILSRCQRFDFKRIPLEDIVERLKKILDKEGI-  194 (355)
T ss_pred             CCceEEEEeChhhcCHHHHHHHHHHHhCCccceeEEEEeCCHHHHHHHHHhheeEEEcCCCCHHHHHHHHHHHHHHcCC-
Confidence            34558999999765  3466666666544456667777755442 2222 34567889999999988888776532221 


Q ss_pred             CccHHHHHHHHHHHhCCCchHHHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLALKVL  167 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai~~~  167 (192)
                       .-.++.+..+++.++|.|..+...
T Consensus       195 -~i~~~a~~~l~~~~~g~~~~a~~~  218 (355)
T TIGR02397       195 -KIEDEALELIARAADGSLRDALSL  218 (355)
T ss_pred             -CCCHHHHHHHHHHcCCChHHHHHH
Confidence             122456667788888887654433

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.

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.53  E-value=0.004  Score=52.91  Aligned_cols=100  Identities=9%  Similarity=0.064  Sum_probs=62.5

Q ss_pred             CceEEEEEeCCCCc--hhHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCF--SQLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +++-++|+|+++..  ...+.|...+........+|++|.+.. +...+ +....+++++++.++....+...+....  
T Consensus       118 g~~kVIIIDEad~Lt~~a~naLLk~LEEP~~~~ifILaTt~~~kll~TI~SRcq~i~F~pLs~~eL~~~L~~il~~eg--  195 (624)
T PRK14959        118 GRYKVFIIDEAHMLTREAFNALLKTLEEPPARVTFVLATTEPHKFPVTIVSRCQHFTFTRLSEAGLEAHLTKVLGREG--  195 (624)
T ss_pred             CCceEEEEEChHhCCHHHHHHHHHHhhccCCCEEEEEecCChhhhhHHHHhhhhccccCCCCHHHHHHHHHHHHHHcC--
Confidence            45669999999865  346677666654445566666665533 22222 3346789999999999888877553221  


Q ss_pred             CccHHHHHHHHHHHhCCCc-hHHHHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIP-LALKVLS  168 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~P-lai~~~~  168 (192)
                      ..-..+.+..|++.++|.+ .|+..+.
T Consensus       196 i~id~eal~lIA~~s~GdlR~Al~lLe  222 (624)
T PRK14959        196 VDYDPAAVRLIARRAAGSVRDSMSLLG  222 (624)
T ss_pred             CCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            1123445667777788754 4555554

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.51  E-value=0.0078  Score=49.83  Aligned_cols=101  Identities=17%  Similarity=0.132  Sum_probs=60.7

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +++-++|+|+++...  ..+.+...+......+.+|++|.+.. +.... .....+.+.+++.++....+...+....  
T Consensus       116 ~~~kVvIIDE~h~Lt~~a~~~LLk~LE~p~~~vv~Ilattn~~kl~~~L~SR~~vv~f~~l~~~el~~~L~~i~~~eg--  193 (472)
T PRK14962        116 GKYKVYIIDEVHMLTKEAFNALLKTLEEPPSHVVFVLATTNLEKVPPTIISRCQVIEFRNISDELIIKRLQEVAEAEG--  193 (472)
T ss_pred             CCeEEEEEEChHHhHHHHHHHHHHHHHhCCCcEEEEEEeCChHhhhHHHhcCcEEEEECCccHHHHHHHHHHHHHHcC--
Confidence            456699999998553  35666666554444455555554422 22222 4557899999999998888887663221  


Q ss_pred             CccHHHHHHHHHHHhCCC-chHHHHHHH
Q 039644          143 DVGYEKLSSNVTKYAQGI-PLALKVLSC  169 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~-Plai~~~~~  169 (192)
                      -.-.++....|++.++|. +.|+..+-.
T Consensus       194 i~i~~eal~~Ia~~s~GdlR~aln~Le~  221 (472)
T PRK14962        194 IEIDREALSFIAKRASGGLRDALTMLEQ  221 (472)
T ss_pred             CCCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            122344556677766544 556555544

>PRK08116 hypothetical protein; Validated

Probab=97.51  E-value=0.00054  Score=52.46  Aligned_cols=92  Identities=18%  Similarity=0.168  Sum_probs=51.4

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCC--
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVT--   78 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~--   78 (192)
                      +|||.||..+++.+..+...++++.           ..+++..+.........  .....+...+.+-. ||||||+.  
T Consensus       125 tGKThLa~aia~~l~~~~~~v~~~~-----------~~~ll~~i~~~~~~~~~--~~~~~~~~~l~~~d-lLviDDlg~e  190 (268)
T PRK08116        125 TGKTYLAACIANELIEKGVPVIFVN-----------FPQLLNRIKSTYKSSGK--EDENEIIRSLVNAD-LLILDDLGAE  190 (268)
T ss_pred             CCHHHHHHHHHHHHHHcCCeEEEEE-----------HHHHHHHHHHHHhcccc--ccHHHHHHHhcCCC-EEEEecccCC
Confidence            6999999999998765544445553           34455555444332211  12333445555444 89999994  


Q ss_pred             CchhHH--HhhccCCC-CCCCceEEEEecch
Q 039644           79 CFSQLE--SLMGSLDW-LTPVSRIILTTRNK  106 (192)
Q Consensus        79 ~~~~~~--~l~~~~~~-~~~~~~iivTtR~~  106 (192)
                      ...+|.  .+...+.. ...+..+|+||...
T Consensus       191 ~~t~~~~~~l~~iin~r~~~~~~~IiTsN~~  221 (268)
T PRK08116        191 RDTEWAREKVYNIIDSRYRKGLPTIVTTNLS  221 (268)
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCCEEEECCCC
Confidence            333332  22222211 23456789998754

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.49  E-value=0.0049  Score=50.63  Aligned_cols=120  Identities=13%  Similarity=0.143  Sum_probs=68.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||+|++.+++.+......++++.           ..++...+...+...     ....++..+++ .-+|++||+...
T Consensus       152 ~GKTHLl~Ai~~~l~~~~~~v~yi~-----------~~~f~~~~~~~l~~~-----~~~~f~~~~~~-~dvLiIDDiq~l  214 (445)
T PRK12422        152 SGKTHLMQAAVHALRESGGKILYVR-----------SELFTEHLVSAIRSG-----EMQRFRQFYRN-VDALFIEDIEVF  214 (445)
T ss_pred             CCHHHHHHHHHHHHHHcCCCEEEee-----------HHHHHHHHHHHHhcc-----hHHHHHHHccc-CCEEEEcchhhh
Confidence            6999999999998765433445553           233444444443221     12334444433 347888999743


Q ss_pred             hh----HHHhhccCCC-CCCCceEEEEecch---------hHHhhcCCCceEecCCCCHHHHHHHHHHhhc
Q 039644           81 SQ----LESLMGSLDW-LTPVSRIILTTRNK---------QVLRNWGVSKIYEMEALEYHHALELFSQHAF  137 (192)
Q Consensus        81 ~~----~~~l~~~~~~-~~~~~~iivTtR~~---------~~~~~~~~~~~~~l~~l~~~ea~~lf~~~~~  137 (192)
                      ..    .+.+...+.. ...|..||+||...         .+...+..+-.+.+++++.++-..++.+.+-
T Consensus       215 ~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l~~rL~SR~~~Gl~~~l~~pd~e~r~~iL~~k~~  285 (445)
T PRK12422        215 SGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLISRFEWGIAIPLHPLTKEGLRSFLERKAE  285 (445)
T ss_pred             cCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhhHHHHHhhhcCCeEEecCCCCHHHHHHHHHHHHH
Confidence            21    1222221110 12355788888542         1222223456888999999999999888764

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.46  E-value=0.0012  Score=49.14  Aligned_cols=100  Identities=14%  Similarity=0.121  Sum_probs=56.1

Q ss_pred             EEEEEeCCCCchh--HHHhhccCCCC-CCCc-eEEEEecchhHHh--------hcCCCceEecCCCCHHHHHHHHHHhhc
Q 039644           70 VLIVFDDVTCFSQ--LESLMGSLDWL-TPVS-RIILTTRNKQVLR--------NWGVSKIYEMEALEYHHALELFSQHAF  137 (192)
Q Consensus        70 ~LlVlDdv~~~~~--~~~l~~~~~~~-~~~~-~iivTtR~~~~~~--------~~~~~~~~~l~~l~~~ea~~lf~~~~~  137 (192)
                      -++|+||++....  -..+...+... ..+. .+|+|++......        .+.....+.+++++.++-..++.+.+-
T Consensus        92 ~~liiDdi~~l~~~~~~~L~~~~~~~~~~~~~~vl~~~~~~~~~~~l~~~L~sr~~~~~~i~l~pl~~~~~~~~l~~~~~  171 (227)
T PRK08903         92 ELYAVDDVERLDDAQQIALFNLFNRVRAHGQGALLVAGPAAPLALPLREDLRTRLGWGLVYELKPLSDADKIAALKAAAA  171 (227)
T ss_pred             CEEEEeChhhcCchHHHHHHHHHHHHHHcCCcEEEEeCCCCHHhCCCCHHHHHHHhcCeEEEecCCCHHHHHHHHHHHHH
Confidence            3799999975422  22232222211 1333 3666665432111        222246789999998877776665432


Q ss_pred             CCCCCCccHHHHHHHHHHHhCCCchHHHHHHHHh
Q 039644          138 KRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFL  171 (192)
Q Consensus       138 ~~~~~~~~~~~~~~~i~~~~~g~Plai~~~~~~l  171 (192)
                      ...  -.-.++....+.+.+.|.+..+..+...|
T Consensus       172 ~~~--v~l~~~al~~L~~~~~gn~~~l~~~l~~l  203 (227)
T PRK08903        172 ERG--LQLADEVPDYLLTHFRRDMPSLMALLDAL  203 (227)
T ss_pred             HcC--CCCCHHHHHHHHHhccCCHHHHHHHHHHH
Confidence            211  22234566677788899988876666554

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

Probab=97.45  E-value=0.0042  Score=53.97  Aligned_cols=136  Identities=18%  Similarity=0.249  Sum_probs=73.0

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhc--CCceEEEEEeCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRL--SRMKVLIVFDDVT   78 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l--~~~~~LlVlDdv~   78 (192)
                      +||||||+.+++.....|..   +.   ...   ..+.++ ..++..             ....+  .+++.+|+||+++
T Consensus        63 tGKTTLA~aIA~~~~~~f~~---ln---a~~---~~i~di-r~~i~~-------------a~~~l~~~~~~~IL~IDEIh  119 (725)
T PRK13341         63 VGKTTLARIIANHTRAHFSS---LN---AVL---AGVKDL-RAEVDR-------------AKERLERHGKRTILFIDEVH  119 (725)
T ss_pred             CCHHHHHHHHHHHhcCccee---eh---hhh---hhhHHH-HHHHHH-------------HHHHhhhcCCceEEEEeChh
Confidence            69999999999987665521   11   100   112221 111111             11111  2356799999998


Q ss_pred             Cc--hhHHHhhccCCCCCCCceEEEE--ecchhH--Hh-hcCCCceEecCCCCHHHHHHHHHHhhcC-----CCCCCccH
Q 039644           79 CF--SQLESLMGSLDWLTPVSRIILT--TRNKQV--LR-NWGVSKIYEMEALEYHHALELFSQHAFK-----RNHPDVGY  146 (192)
Q Consensus        79 ~~--~~~~~l~~~~~~~~~~~~iivT--tR~~~~--~~-~~~~~~~~~l~~l~~~ea~~lf~~~~~~-----~~~~~~~~  146 (192)
                      ..  ...+.+...+.   .++.+++.  |.+...  .. ..+....+.+++++.++...++.+..-.     +.....-.
T Consensus       120 ~Ln~~qQdaLL~~lE---~g~IiLI~aTTenp~~~l~~aL~SR~~v~~l~pLs~edi~~IL~~~l~~~~~~~g~~~v~I~  196 (725)
T PRK13341        120 RFNKAQQDALLPWVE---NGTITLIGATTENPYFEVNKALVSRSRLFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLE  196 (725)
T ss_pred             hCCHHHHHHHHHHhc---CceEEEEEecCCChHhhhhhHhhccccceecCCCCHHHHHHHHHHHHHHHHhhcCCcccCCC
Confidence            54  34556654432   34445553  333221  11 1133567999999999999998876531     01111223


Q ss_pred             HHHHHHHHHHhCCCch
Q 039644          147 EKLSSNVTKYAQGIPL  162 (192)
Q Consensus       147 ~~~~~~i~~~~~g~Pl  162 (192)
                      ++....|++.+.|...
T Consensus       197 deaL~~La~~s~GD~R  212 (725)
T PRK13341        197 PEAEKHLVDVANGDAR  212 (725)
T ss_pred             HHHHHHHHHhCCCCHH
Confidence            4455667777776533

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

Probab=97.44  E-value=0.0025  Score=50.42  Aligned_cols=141  Identities=17%  Similarity=0.276  Sum_probs=82.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +||||||+.++..-+.+-  ..||. .+.+.   .+..++. .+.++-..           ...+..++.+|.+|.+..-
T Consensus       173 ~GKTtlArlia~tsk~~S--yrfve-lSAt~---a~t~dvR-~ife~aq~-----------~~~l~krkTilFiDEiHRF  234 (554)
T KOG2028|consen  173 TGKTTLARLIASTSKKHS--YRFVE-LSATN---AKTNDVR-DIFEQAQN-----------EKSLTKRKTILFIDEIHRF  234 (554)
T ss_pred             CchHHHHHHHHhhcCCCc--eEEEE-Eeccc---cchHHHH-HHHHHHHH-----------HHhhhcceeEEEeHHhhhh
Confidence            699999999999766542  45555 33322   2233322 22222211           1233567889999999643


Q ss_pred             --hhHHHhhccCCCCCCCceEEE--EecchhHHhh---cCCCceEecCCCCHHHHHHHHHHhhc---CCCC-----CC--
Q 039644           81 --SQLESLMGSLDWLTPVSRIIL--TTRNKQVLRN---WGVSKIYEMEALEYHHALELFSQHAF---KRNH-----PD--  143 (192)
Q Consensus        81 --~~~~~l~~~~~~~~~~~~iiv--TtR~~~~~~~---~~~~~~~~l~~l~~~ea~~lf~~~~~---~~~~-----~~--  143 (192)
                        .+-+-|   +|...+|+-++|  ||.+++....   .+...++-|+.|+.++...++.+..-   .+..     +.  
T Consensus       235 NksQQD~f---LP~VE~G~I~lIGATTENPSFqln~aLlSRC~VfvLekL~~n~v~~iL~raia~l~dser~~~~l~n~s  311 (554)
T KOG2028|consen  235 NKSQQDTF---LPHVENGDITLIGATTENPSFQLNAALLSRCRVFVLEKLPVNAVVTILMRAIASLGDSERPTDPLPNSS  311 (554)
T ss_pred             hhhhhhcc---cceeccCceEEEecccCCCccchhHHHHhccceeEeccCCHHHHHHHHHHHHHhhccccccCCCCCCcc
Confidence              333444   455567776666  6777654333   25678999999999999888877332   1111     11  


Q ss_pred             -ccHHHHHHHHHHHhCCCch
Q 039644          144 -VGYEKLSSNVTKYAQGIPL  162 (192)
Q Consensus       144 -~~~~~~~~~i~~~~~g~Pl  162 (192)
                       .-.+.+.+-++..|+|--.
T Consensus       312 ~~ve~siidyla~lsdGDaR  331 (554)
T KOG2028|consen  312 MFVEDSIIDYLAYLSDGDAR  331 (554)
T ss_pred             hhhhHHHHHHHHHhcCchHH
Confidence             1234455556666777643

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.39  E-value=0.013  Score=50.01  Aligned_cols=97  Identities=12%  Similarity=0.107  Sum_probs=61.6

Q ss_pred             CceEEEEEeCCCCc--hhHHHhhccCCCCCCCceEEEEecch-hHHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCF--SQLESLMGSLDWLTPVSRIILTTRNK-QVLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~iivTtR~~-~~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      ..+-++|+|+++..  ...+.|...+.+....+.+|+++.+. .+.... +....+.+..++..+....+.+.+..... 
T Consensus       119 ~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~tv~Il~t~~~~kll~tI~SR~~~i~f~~l~~~el~~~L~~~a~~egl-  197 (585)
T PRK14950        119 ARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHKVPATILSRCQRFDFHRHSVADMAAHLRKIAAAEGI-  197 (585)
T ss_pred             CCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCeEEEEEeCChhhhhHHHHhccceeeCCCCCHHHHHHHHHHHHHHcCC-
Confidence            45668999999865  34666766655545566676666443 222222 34567889999999988888776543221 


Q ss_pred             CccHHHHHHHHHHHhCCCchHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLALK  165 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai~  165 (192)
                       ....+.+..+++.++|.+..+.
T Consensus       198 -~i~~eal~~La~~s~Gdlr~al  219 (585)
T PRK14950        198 -NLEPGALEAIARAATGSMRDAE  219 (585)
T ss_pred             -CCCHHHHHHHHHHcCCCHHHHH
Confidence             1223556678888888776443

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=97.36  E-value=0.01  Score=50.55  Aligned_cols=98  Identities=15%  Similarity=0.160  Sum_probs=62.7

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecc-hhHHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRN-KQVLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~-~~~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +++-++|+|+++...  ..+.|...+.+....+++|++|.. ..+...+ +....+.+..++.++....+...+-...  
T Consensus       131 a~~KVvIIDEad~Ls~~a~naLLKtLEePp~~~~fIl~tte~~kll~tI~SRcq~~~f~~l~~~el~~~L~~i~~keg--  208 (598)
T PRK09111        131 ARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHVKFIFATTEIRKVPVTVLSRCQRFDLRRIEADVLAAHLSRIAAKEG--  208 (598)
T ss_pred             CCcEEEEEEChHhCCHHHHHHHHHHHHhCCCCeEEEEEeCChhhhhHHHHhheeEEEecCCCHHHHHHHHHHHHHHcC--
Confidence            345589999998654  467777666655566777766633 2222222 4457899999999998888877653221  


Q ss_pred             CccHHHHHHHHHHHhCCCchHHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLALKV  166 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai~~  166 (192)
                      .....+....|++.++|.+.-+..
T Consensus       209 i~i~~eAl~lIa~~a~Gdlr~al~  232 (598)
T PRK09111        209 VEVEDEALALIARAAEGSVRDGLS  232 (598)
T ss_pred             CCCCHHHHHHHHHHcCCCHHHHHH
Confidence            112235566778888887765443

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.36  E-value=0.0059  Score=49.49  Aligned_cols=96  Identities=10%  Similarity=0.106  Sum_probs=61.3

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecc-hhHHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRN-KQVLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~-~~~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +.+-++|+|+++...  .++.+...+.+..+.+.+|++|.. ..+.... .....+++.+++.++....+...+-...  
T Consensus       126 ~~~kvvIIdea~~l~~~~~~~LLk~LEep~~~t~~Il~t~~~~kl~~tl~sR~~~v~f~~l~~~ei~~~l~~~~~~~g--  203 (397)
T PRK14955        126 GRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQRFNFKRIPLEEIQQQLQGICEAEG--  203 (397)
T ss_pred             CCeEEEEEeChhhCCHHHHHHHHHHHhcCCCCeEEEEEeCChHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHcC--
Confidence            455689999998654  577777776655566676666533 3333222 3346788999999998887776552211  


Q ss_pred             CccHHHHHHHHHHHhCCCchHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLAL  164 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai  164 (192)
                      ..-.++.+..+++.++|.+--+
T Consensus       204 ~~i~~~al~~l~~~s~g~lr~a  225 (397)
T PRK14955        204 ISVDADALQLIGRKAQGSMRDA  225 (397)
T ss_pred             CCCCHHHHHHHHHHcCCCHHHH
Confidence            1233556677888888877533

>TIGR00767 rho transcription termination factor Rho

Probab=97.34  E-value=0.00071  Score=54.30  Aligned_cols=77  Identities=19%  Similarity=0.270  Sum_probs=51.4

Q ss_pred             CchhHHHHHHHHHhhC-CCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-cC---------chHHHHhh-cCCc
Q 039644            1 IGKTAIARAIFDKISG-DFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV-MP---------YIDLNFRR-LSRM   68 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~-~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~---------~~~~l~~~-l~~~   68 (192)
                      +|||||++.+++.+.. +|+..+|+.++++   .+..+.+++..++..+.....+ ..         ..+..... -.++
T Consensus       179 ~GKTtL~~~i~~~I~~nhfdv~v~VlLIgE---R~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v~e~Ae~~~~~Gk  255 (415)
T TIGR00767       179 AGKTVLLQKIAQAITRNHPEVELIVLLIDE---RPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVIEKAKRLVEHKK  255 (415)
T ss_pred             CChhHHHHHHHHhhcccCCceEEEEEEcCC---CCccHHHHHHHhhceEEEecCCCChHHHHHHHHHHHHHHHHHHHcCC
Confidence            5999999999997654 4999999986533   2357888888885544332222 11         22222222 2578


Q ss_pred             eEEEEEeCCCCc
Q 039644           69 KVLIVFDDVTCF   80 (192)
Q Consensus        69 ~~LlVlDdv~~~   80 (192)
                      +.+|++|.+...
T Consensus       256 dVVLlIDEitR~  267 (415)
T TIGR00767       256 DVVILLDSITRL  267 (415)
T ss_pred             CeEEEEEChhHH
Confidence            999999999744

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

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.32  E-value=0.031  Score=46.55  Aligned_cols=96  Identities=11%  Similarity=0.095  Sum_probs=58.2

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecch-hHHhh-cCCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNK-QVLRN-WGVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~-~~~~~-~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +++-++|+|+++...  ..+.+...+......+.+|++|.+. .+... ......+.+.+++.++....+...+-.... 
T Consensus       118 ~~~KVvIIDEad~Lt~~a~naLLk~LEepp~~~v~Il~tt~~~kl~~tI~SRc~~i~f~~ls~~el~~~L~~i~k~egi-  196 (486)
T PRK14953        118 GKYKVYIIDEAHMLTKEAFNALLKTLEEPPPRTIFILCTTEYDKIPPTILSRCQRFIFSKPTKEQIKEYLKRICNEEKI-  196 (486)
T ss_pred             CCeeEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEECCHHHHHHHHHHhceEEEcCCCCHHHHHHHHHHHHHHcCC-
Confidence            456699999998553  4566666655544455566555432 22222 134567999999999988877775532221 


Q ss_pred             CccHHHHHHHHHHHhCCCchHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLAL  164 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai  164 (192)
                       ....+....+++.++|.+..+
T Consensus       197 -~id~~al~~La~~s~G~lr~a  217 (486)
T PRK14953        197 -EYEEKALDLLAQASEGGMRDA  217 (486)
T ss_pred             -CCCHHHHHHHHHHcCCCHHHH
Confidence             122344556777777766543

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=97.30  E-value=0.0084  Score=50.78  Aligned_cols=93  Identities=15%  Similarity=0.136  Sum_probs=56.9

Q ss_pred             ceEEEEEeCCCCc--hhHHHhhccCCCCCCCceEEEEecch-hHHhh-cCCCceEecCCCCHHHHHHHHHHhhcCCCCCC
Q 039644           68 MKVLIVFDDVTCF--SQLESLMGSLDWLTPVSRIILTTRNK-QVLRN-WGVSKIYEMEALEYHHALELFSQHAFKRNHPD  143 (192)
Q Consensus        68 ~~~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~iivTtR~~-~~~~~-~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~  143 (192)
                      ++-++|+|+++..  ..+..+...+......+.+|++|... .+... .+....+++.+++.++....+...+....  .
T Consensus       119 ~~KVIIIDEad~Lt~~A~NaLLKtLEEPp~~tvfIL~Tt~~~KLl~TI~SRcq~ieF~~Ls~~eL~~~L~~il~keg--i  196 (605)
T PRK05896        119 KYKVYIIDEAHMLSTSAWNALLKTLEEPPKHVVFIFATTEFQKIPLTIISRCQRYNFKKLNNSELQELLKSIAKKEK--I  196 (605)
T ss_pred             CcEEEEEechHhCCHHHHHHHHHHHHhCCCcEEEEEECCChHhhhHHHHhhhhhcccCCCCHHHHHHHHHHHHHHcC--C
Confidence            3447999999865  34666666555444455566555433 22222 24457899999999998888877553221  1


Q ss_pred             ccHHHHHHHHHHHhCCCch
Q 039644          144 VGYEKLSSNVTKYAQGIPL  162 (192)
Q Consensus       144 ~~~~~~~~~i~~~~~g~Pl  162 (192)
                      .-..+.+..+++.++|.+.
T Consensus       197 ~Is~eal~~La~lS~GdlR  215 (605)
T PRK05896        197 KIEDNAIDKIADLADGSLR  215 (605)
T ss_pred             CCCHHHHHHHHHHcCCcHH
Confidence            1223446677777887654

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.30  E-value=0.019  Score=48.78  Aligned_cols=94  Identities=14%  Similarity=0.144  Sum_probs=58.6

Q ss_pred             CceEEEEEeCCCCc--hhHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCF--SQLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      ++.-++|+|+++..  ...+.|...+......+.+|++|.+.. +...+ +....+.+.+++.++..+.+...+..... 
T Consensus       117 ~~~KVvIIDEah~Lt~~A~NALLK~LEEpp~~~~fIL~tte~~kll~TI~SRc~~~~F~~l~~~~i~~~L~~i~~~egi-  195 (584)
T PRK14952        117 SRYRIFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKVLPTIRSRTHHYPFRLLPPRTMRALIARICEQEGV-  195 (584)
T ss_pred             CCceEEEEECCCcCCHHHHHHHHHHHhcCCCCeEEEEEeCChHhhHHHHHHhceEEEeeCCCHHHHHHHHHHHHHHcCC-
Confidence            34558999999855  346777777666556666666664432 22222 44678999999999988877765532221 


Q ss_pred             CccHHHHHHHHHHHhCCCch
Q 039644          143 DVGYEKLSSNVTKYAQGIPL  162 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Pl  162 (192)
                       ....+....|++.++|.+.
T Consensus       196 -~i~~~al~~Ia~~s~GdlR  214 (584)
T PRK14952        196 -VVDDAVYPLVIRAGGGSPR  214 (584)
T ss_pred             -CCCHHHHHHHHHHcCCCHH
Confidence             1123344556667777654

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=97.23  E-value=0.052  Score=42.67  Aligned_cols=93  Identities=14%  Similarity=0.167  Sum_probs=62.6

Q ss_pred             CceEEEEEeCCCCchh--HHHhhccCCCCCCCceEEEEecchhH-Hhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFSQ--LESLMGSLDWLTPVSRIILTTRNKQV-LRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~~--~~~l~~~~~~~~~~~~iivTtR~~~~-~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +++-++|+|+++....  -..+...+-+-..++.+|++|.+... ...+ +....+.+.+++.+++.+.+....   .. 
T Consensus       112 g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~~~~lLpTIrSRCq~i~~~~~~~~~~~~~L~~~~---~~-  187 (319)
T PRK08769        112 GIAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPARLPATIRSRCQRLEFKLPPAHEALAWLLAQG---VS-  187 (319)
T ss_pred             CCcEEEEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECChhhCchHHHhhheEeeCCCcCHHHHHHHHHHcC---CC-
Confidence            3456899999997653  56666666655667878888876442 2222 456789999999999888876531   11 


Q ss_pred             CccHHHHHHHHHHHhCCCchHHHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLALKVL  167 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai~~~  167 (192)
                          ...+..++..++|.|+....+
T Consensus       188 ----~~~a~~~~~l~~G~p~~A~~~  208 (319)
T PRK08769        188 ----ERAAQEALDAARGHPGLAAQW  208 (319)
T ss_pred             ----hHHHHHHHHHcCCCHHHHHHH
Confidence                222556788999999855443

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.20  E-value=0.025  Score=45.28  Aligned_cols=94  Identities=15%  Similarity=0.205  Sum_probs=54.3

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecch-hHHhh-cCCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNK-QVLRN-WGVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~-~~~~~-~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +++-++++|+++...  .++.+...+......+.+|+++... ..... .+....++..+++.++....+...+..... 
T Consensus       107 ~~~kiviIDE~~~l~~~~~~~ll~~le~~~~~~~~Il~~~~~~kl~~~l~sr~~~v~~~~~~~~~l~~~l~~~~~~~g~-  185 (367)
T PRK14970        107 GKYKIYIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHKIIPTILSRCQIFDFKRITIKDIKEHLAGIAVKEGI-  185 (367)
T ss_pred             CCcEEEEEeChhhcCHHHHHHHHHHHhCCCCceEEEEEeCCcccCCHHHHhcceeEecCCccHHHHHHHHHHHHHHcCC-
Confidence            345589999997543  3666655554434455566655332 22211 134467899999999988888775532221 


Q ss_pred             CccHHHHHHHHHHHhCCCch
Q 039644          143 DVGYEKLSSNVTKYAQGIPL  162 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Pl  162 (192)
                       .-.++....+++.++|.+-
T Consensus       186 -~i~~~al~~l~~~~~gdlr  204 (367)
T PRK14970        186 -KFEDDALHIIAQKADGALR  204 (367)
T ss_pred             -CCCHHHHHHHHHhCCCCHH
Confidence             1123445556666666544

>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=97.15  E-value=0.0043  Score=42.00  Aligned_cols=94  Identities=18%  Similarity=0.137  Sum_probs=46.6

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||++++.+++.....-..++++. .....    ...... ......    .   ...........++.++++|+++..
T Consensus        30 ~GKT~l~~~i~~~~~~~~~~v~~~~-~~~~~----~~~~~~-~~~~~~----~---~~~~~~~~~~~~~~~lilDe~~~~   96 (151)
T cd00009          30 TGKTTLARAIANELFRPGAPFLYLN-ASDLL----EGLVVA-ELFGHF----L---VRLLFELAEKAKPGVLFIDEIDSL   96 (151)
T ss_pred             CCHHHHHHHHHHHhhcCCCCeEEEe-hhhhh----hhhHHH-HHhhhh----h---HhHHHHhhccCCCeEEEEeChhhh
Confidence            6999999999998754334455554 22211    111111 000000    0   000111222456789999999854


Q ss_pred             -----hhHHHhhccCCCC---CCCceEEEEecchh
Q 039644           81 -----SQLESLMGSLDWL---TPVSRIILTTRNKQ  107 (192)
Q Consensus        81 -----~~~~~l~~~~~~~---~~~~~iivTtR~~~  107 (192)
                           ..+..........   ..+..+|+||....
T Consensus        97 ~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~  131 (151)
T cd00009          97 SRGAQNALLRVLETLNDLRIDRENVRVIGATNRPL  131 (151)
T ss_pred             hHHHHHHHHHHHHhcCceeccCCCeEEEEecCccc
Confidence                 1223322323221   35678888887543

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

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=97.13  E-value=0.018  Score=50.83  Aligned_cols=162  Identities=12%  Similarity=0.108  Sum_probs=85.0

Q ss_pred             CchhHHHHHHHHHhhCC-----Cc--ceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC--cC---chHHHHhhcC--
Q 039644            1 IGKTAIARAIFDKISGD-----FE--CSCFLENVREESQRPGGLACLRQKLLSNILKDKNV--MP---YIDLNFRRLS--   66 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~-----F~--~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--~~---~~~~l~~~l~--   66 (192)
                      +|||++++.|.+++.+.     .+  .++++.+..-     .....++..|..++....+.  ..   ....+...+.  
T Consensus       792 TGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~L-----stp~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~  866 (1164)
T PTZ00112        792 TGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNV-----VHPNAAYQVLYKQLFNKKPPNALNSFKILDRLFNQNKKD  866 (1164)
T ss_pred             CCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCcc-----CCHHHHHHHHHHHHcCCCCCccccHHHHHHHHHhhhhcc
Confidence            59999999999865321     22  2345542221     46777888888888544333  22   3334444432  


Q ss_pred             -CceEEEEEeCCCCch-----hHHHhhccCCCCCCCceEEE--Eecchh--------HHhhcCCCceEecCCCCHHHHHH
Q 039644           67 -RMKVLIVFDDVTCFS-----QLESLMGSLDWLTPVSRIIL--TTRNKQ--------VLRNWGVSKIYEMEALEYHHALE  130 (192)
Q Consensus        67 -~~~~LlVlDdv~~~~-----~~~~l~~~~~~~~~~~~iiv--TtR~~~--------~~~~~~~~~~~~l~~l~~~ea~~  130 (192)
                       ....+||||+++...     .+..|... +. ..+++|++  +|....        +...++ ...+..++.+.++..+
T Consensus       867 ~r~v~IIILDEID~L~kK~QDVLYnLFR~-~~-~s~SKLiLIGISNdlDLperLdPRLRSRLg-~eeIvF~PYTaEQL~d  943 (1164)
T PTZ00112        867 NRNVSILIIDEIDYLITKTQKVLFTLFDW-PT-KINSKLVLIAISNTMDLPERLIPRCRSRLA-FGRLVFSPYKGDEIEK  943 (1164)
T ss_pred             cccceEEEeehHhhhCccHHHHHHHHHHH-hh-ccCCeEEEEEecCchhcchhhhhhhhhccc-cccccCCCCCHHHHHH
Confidence             224699999998432     12222222 11 23445554  332211        111112 2236679999999999


Q ss_pred             HHHHhhcCCC--CCCccHHHHHHHHHHHhCCCchHHHHHHHH
Q 039644          131 LFSQHAFKRN--HPDVGYEKLSSNVTKYAQGIPLALKVLSCF  170 (192)
Q Consensus       131 lf~~~~~~~~--~~~~~~~~~~~~i~~~~~g~Plai~~~~~~  170 (192)
                      ++..++....  ..+..++..+..++...|..-.||.++-..
T Consensus       944 ILk~RAe~A~gVLdDdAIELIArkVAq~SGDARKALDILRrA  985 (1164)
T PTZ00112        944 IIKERLENCKEIIDHTAIQLCARKVANVSGDIRKALQICRKA  985 (1164)
T ss_pred             HHHHHHHhCCCCCCHHHHHHHHHhhhhcCCHHHHHHHHHHHH
Confidence            9998875321  122233333333333334445555554433

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.10  E-value=0.033  Score=47.66  Aligned_cols=94  Identities=11%  Similarity=0.105  Sum_probs=59.2

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecc-hhHHhh-cCCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRN-KQVLRN-WGVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~-~~~~~~-~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +.+-++|+|+++...  ..+.|...+.+....+.+|++|.. ..+... ......+++.+++.++....+...+-...  
T Consensus       126 ~~~KVvIIdEad~Lt~~a~naLLK~LEePp~~tv~IL~t~~~~kLl~TI~SRc~~vef~~l~~~ei~~~L~~i~~~eg--  203 (620)
T PRK14954        126 GRYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQRFNFKRIPLDEIQSQLQMICRAEG--  203 (620)
T ss_pred             CCCEEEEEeChhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhHHHHhhceEEecCCCCHHHHHHHHHHHHHHcC--
Confidence            345588999998654  467777766665555666655543 333222 24567899999999998877766543211  


Q ss_pred             CccHHHHHHHHHHHhCCCch
Q 039644          143 DVGYEKLSSNVTKYAQGIPL  162 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Pl  162 (192)
                      ..-..+.+..+++.++|..-
T Consensus       204 i~I~~eal~~La~~s~Gdlr  223 (620)
T PRK14954        204 IQIDADALQLIARKAQGSMR  223 (620)
T ss_pred             CCCCHHHHHHHHHHhCCCHH
Confidence            11234556677788888554

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=97.09  E-value=0.035  Score=46.61  Aligned_cols=96  Identities=10%  Similarity=0.124  Sum_probs=60.2

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchhHHh-h-cCCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQVLR-N-WGVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~~~~-~-~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +.+-++|+|+++...  ..+.+...+......+++|++|.+..-.. . .+....+++.+++.++....+...+..... 
T Consensus       116 ~~~KVvIIDEad~Lt~~A~NALLK~LEEpp~~t~FIL~ttd~~kL~~tI~SRc~~~~F~~Ls~~ei~~~L~~Il~~EGi-  194 (535)
T PRK08451        116 ARFKIFIIDEVHMLTKEAFNALLKTLEEPPSYVKFILATTDPLKLPATILSRTQHFRFKQIPQNSIISHLKTILEKEGV-  194 (535)
T ss_pred             CCeEEEEEECcccCCHHHHHHHHHHHhhcCCceEEEEEECChhhCchHHHhhceeEEcCCCCHHHHHHHHHHHHHHcCC-
Confidence            345589999998654  35666666655556677777776542111 1 134578999999999988887765532221 


Q ss_pred             CccHHHHHHHHHHHhCCCchHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLAL  164 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai  164 (192)
                       ....+....|++.++|.+.-+
T Consensus       195 -~i~~~Al~~Ia~~s~GdlR~a  215 (535)
T PRK08451        195 -SYEPEALEILARSGNGSLRDT  215 (535)
T ss_pred             -CCCHHHHHHHHHHcCCcHHHH
Confidence             112345566777777776443

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=97.02  E-value=0.048  Score=46.24  Aligned_cols=95  Identities=9%  Similarity=0.136  Sum_probs=59.7

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecch-hHHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNK-QVLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~-~~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +++-++|+|+++...  .++.+...+......+.+|.+|... .+.... +....++..+++.++....+...+....  
T Consensus       118 ~~~KVvIIDEa~~Ls~~a~naLLK~LEepp~~~vfI~~tte~~kL~~tI~SRc~~~~f~~l~~~el~~~L~~i~~~eg--  195 (563)
T PRK06647        118 SRYRVYIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTEVHKLPATIKSRCQHFNFRLLSLEKIYNMLKKVCLEDQ--  195 (563)
T ss_pred             CCCEEEEEEChhhcCHHHHHHHHHhhccCCCCEEEEEecCChHHhHHHHHHhceEEEecCCCHHHHHHHHHHHHHHcC--
Confidence            455689999998654  4677777766555666676666443 222222 4456789999999998888776653222  


Q ss_pred             CccHHHHHHHHHHHhCCCchH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Pla  163 (192)
                      -....+....|++.++|.+..
T Consensus       196 i~id~eAl~lLa~~s~GdlR~  216 (563)
T PRK06647        196 IKYEDEALKWIAYKSTGSVRD  216 (563)
T ss_pred             CCCCHHHHHHHHHHcCCCHHH
Confidence            122344555677777776643

>PRK06620 hypothetical protein; Validated

Probab=97.00  E-value=0.0083  Score=44.41  Aligned_cols=90  Identities=8%  Similarity=0.002  Sum_probs=52.4

Q ss_pred             EEEEEeCCCCchh--HHHhhccCCCCCCCceEEEEecchhH-------HhhcCCCceEecCCCCHHHHHHHHHHhhcCCC
Q 039644           70 VLIVFDDVTCFSQ--LESLMGSLDWLTPVSRIILTTRNKQV-------LRNWGVSKIYEMEALEYHHALELFSQHAFKRN  140 (192)
Q Consensus        70 ~LlVlDdv~~~~~--~~~l~~~~~~~~~~~~iivTtR~~~~-------~~~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~  140 (192)
                      -++++||++..++  +-.+...+.  ..|..+|+|++....       ...+...-++.+++++.++-..++.+.+....
T Consensus        87 d~lliDdi~~~~~~~lf~l~N~~~--e~g~~ilits~~~p~~l~l~~L~SRl~~gl~~~l~~pd~~~~~~~l~k~~~~~~  164 (214)
T PRK06620         87 NAFIIEDIENWQEPALLHIFNIIN--EKQKYLLLTSSDKSRNFTLPDLSSRIKSVLSILLNSPDDELIKILIFKHFSISS  164 (214)
T ss_pred             CEEEEeccccchHHHHHHHHHHHH--hcCCEEEEEcCCCccccchHHHHHHHhCCceEeeCCCCHHHHHHHHHHHHHHcC
Confidence            3788999985443  222222222  345689998875332       22233455799999999988888877664221


Q ss_pred             CCCccHHHHHHHHHHHhCCCchH
Q 039644          141 HPDVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       141 ~~~~~~~~~~~~i~~~~~g~Pla  163 (192)
                        -.-.++...-|++.+.|.--.
T Consensus       165 --l~l~~ev~~~L~~~~~~d~r~  185 (214)
T PRK06620        165 --VTISRQIIDFLLVNLPREYSK  185 (214)
T ss_pred             --CCCCHHHHHHHHHHccCCHHH
Confidence              122344555666666655444

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=96.99  E-value=0.05  Score=44.92  Aligned_cols=94  Identities=12%  Similarity=0.122  Sum_probs=57.6

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecch-hHHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNK-QVLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~-~~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +.+-++|+|+++...  ..+.+...+.+....+.+|++|... .+.... +....+++++++.++....+...+-...  
T Consensus       120 ~~~kvvIIdead~lt~~~~n~LLk~lEep~~~~~~Il~t~~~~kl~~tI~sRc~~v~f~~l~~~el~~~L~~~~~~eg--  197 (451)
T PRK06305        120 SRYKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVKFFLATTEIHKIPGTILSRCQKMHLKRIPEETIIDKLALIAKQEG--  197 (451)
T ss_pred             CCCEEEEEecHHhhCHHHHHHHHHHhhcCCCCceEEEEeCChHhcchHHHHhceEEeCCCCCHHHHHHHHHHHHHHcC--
Confidence            456689999998553  3566666655545566677666432 222221 3457899999999998887776543211  


Q ss_pred             CccHHHHHHHHHHHhCCCch
Q 039644          143 DVGYEKLSSNVTKYAQGIPL  162 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Pl  162 (192)
                      -...++.+..+++.++|.+.
T Consensus       198 ~~i~~~al~~L~~~s~gdlr  217 (451)
T PRK06305        198 IETSREALLPIARAAQGSLR  217 (451)
T ss_pred             CCCCHHHHHHHHHHcCCCHH
Confidence            11233455667777777553

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.97  E-value=0.052  Score=46.55  Aligned_cols=94  Identities=14%  Similarity=0.200  Sum_probs=60.0

Q ss_pred             ceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEec-chhHHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCCC
Q 039644           68 MKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTR-NKQVLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHPD  143 (192)
Q Consensus        68 ~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR-~~~~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~  143 (192)
                      .+-++|+|+++...  .++.|...+......+.+|++|. ...+.... +....+++++++.++....+...+.....  
T Consensus       121 ~~KVvIIdea~~Ls~~a~naLLK~LEepp~~tifIL~tt~~~kIl~tI~SRc~iv~f~~ls~~ei~~~L~~ia~~egi--  198 (614)
T PRK14971        121 KYKIYIIDEVHMLSQAAFNAFLKTLEEPPSYAIFILATTEKHKILPTILSRCQIFDFNRIQVADIVNHLQYVASKEGI--  198 (614)
T ss_pred             CcEEEEEECcccCCHHHHHHHHHHHhCCCCCeEEEEEeCCchhchHHHHhhhheeecCCCCHHHHHHHHHHHHHHcCC--
Confidence            45588999998654  46777776666556666666553 33333322 45678999999999998888765532221  


Q ss_pred             ccHHHHHHHHHHHhCCCchH
Q 039644          144 VGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       144 ~~~~~~~~~i~~~~~g~Pla  163 (192)
                      ....+.+..|++.++|...-
T Consensus       199 ~i~~~al~~La~~s~gdlr~  218 (614)
T PRK14971        199 TAEPEALNVIAQKADGGMRD  218 (614)
T ss_pred             CCCHHHHHHHHHHcCCCHHH
Confidence            12234556777777776543

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.96  E-value=0.032  Score=47.47  Aligned_cols=93  Identities=13%  Similarity=0.174  Sum_probs=56.1

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      ++.-++|+|+++...  ..+.|...+.+....+.+|++|.+.. +.... +....+++.+++.++....+...+....  
T Consensus       118 ~~~KVvIIdev~~Lt~~a~naLLk~LEepp~~~~fIl~t~~~~kl~~tI~SRc~~~~f~~l~~~~i~~~L~~i~~~eg--  195 (576)
T PRK14965        118 SRYKIFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKVPITILSRCQRFDFRRIPLQKIVDRLRYIADQEG--  195 (576)
T ss_pred             CCceEEEEEChhhCCHHHHHHHHHHHHcCCCCeEEEEEeCChhhhhHHHHHhhhhhhcCCCCHHHHHHHHHHHHHHhC--
Confidence            345589999998654  46677666655555666776654432 33222 4456788999999888877766442211  


Q ss_pred             CccHHHHHHHHHHHhCCCc
Q 039644          143 DVGYEKLSSNVTKYAQGIP  161 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~P  161 (192)
                      -.-..+....+++.++|..
T Consensus       196 i~i~~~al~~la~~a~G~l  214 (576)
T PRK14965        196 ISISDAALALVARKGDGSM  214 (576)
T ss_pred             CCCCHHHHHHHHHHcCCCH
Confidence            1112344555666666654

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

Probab=96.95  E-value=0.12  Score=41.59  Aligned_cols=130  Identities=13%  Similarity=0.187  Sum_probs=80.4

Q ss_pred             CchhHHHHHHHHHhhCCCcc--eEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-c---CchHHHHhhcC--CceEEE
Q 039644            1 IGKTAIARAIFDKISGDFEC--SCFLENVREESQRPGGLACLRQKLLSNILKDKNV-M---PYIDLNFRRLS--RMKVLI   72 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~--~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~---~~~~~l~~~l~--~~~~Ll   72 (192)
                      +|||+.++.+++++.+....  .+++.+...     .....++..++..+..-... .   +....+.+.+.  ++..++
T Consensus        53 TGKT~~~~~v~~~l~~~~~~~~~~yINc~~~-----~t~~~i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~~~Iv  127 (366)
T COG1474          53 TGKTATVKFVMEELEESSANVEVVYINCLEL-----RTPYQVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIV  127 (366)
T ss_pred             CCHhHHHHHHHHHHHhhhccCceEEEeeeeC-----CCHHHHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHhcCCeEEE
Confidence            59999999999987655432  466653222     68889999999988633322 2   25566666664  578999


Q ss_pred             EEeCCCCchh-----HHHhhccCCCCCCCceEEE--EecchhHHhhc--------CCCceEecCCCCHHHHHHHHHHhhc
Q 039644           73 VFDDVTCFSQ-----LESLMGSLDWLTPVSRIIL--TTRNKQVLRNW--------GVSKIYEMEALEYHHALELFSQHAF  137 (192)
Q Consensus        73 VlDdv~~~~~-----~~~l~~~~~~~~~~~~iiv--TtR~~~~~~~~--------~~~~~~~l~~l~~~ea~~lf~~~~~  137 (192)
                      |||+++....     +..+.......  .++|++  .+.........        +. ..+..+|-+.+|..+++..++-
T Consensus       128 vLDEid~L~~~~~~~LY~L~r~~~~~--~~~v~vi~i~n~~~~~~~ld~rv~s~l~~-~~I~F~pY~a~el~~Il~~R~~  204 (366)
T COG1474         128 ILDEVDALVDKDGEVLYSLLRAPGEN--KVKVSIIAVSNDDKFLDYLDPRVKSSLGP-SEIVFPPYTAEELYDILRERVE  204 (366)
T ss_pred             EEcchhhhccccchHHHHHHhhcccc--ceeEEEEEEeccHHHHHHhhhhhhhccCc-ceeeeCCCCHHHHHHHHHHHHH
Confidence            9999985422     22332221111  343333  34333222222        22 3378899999999999988764


Q ss_pred             C
Q 039644          138 K  138 (192)
Q Consensus       138 ~  138 (192)
                      .
T Consensus       205 ~  205 (366)
T COG1474         205 E  205 (366)
T ss_pred             h
Confidence            3

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.94  E-value=0.068  Score=45.89  Aligned_cols=97  Identities=18%  Similarity=0.168  Sum_probs=59.4

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +.+-++|+|+++...  .++.|...+......+.+|++|.+.. +...+ +....+.+..++.++....+.+.+..... 
T Consensus       120 ~~~KViIIDEad~Lt~~a~naLLK~LEePp~~tvfIL~t~~~~~llpTIrSRc~~~~f~~l~~~ei~~~L~~ia~kegi-  198 (620)
T PRK14948        120 ARWKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTDPQRVLPTIISRCQRFDFRRIPLEAMVQHLSEIAEKESI-  198 (620)
T ss_pred             CCceEEEEECccccCHHHHHHHHHHHhcCCcCeEEEEEeCChhhhhHHHHhheeEEEecCCCHHHHHHHHHHHHHHhCC-
Confidence            345589999998654  46677666655445566666655432 22222 44577888999998888777765533211 


Q ss_pred             CccHHHHHHHHHHHhCCCchHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLALK  165 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai~  165 (192)
                       ....+....+++.++|.+..+.
T Consensus       199 -~is~~al~~La~~s~G~lr~A~  220 (620)
T PRK14948        199 -EIEPEALTLVAQRSQGGLRDAE  220 (620)
T ss_pred             -CCCHHHHHHHHHHcCCCHHHHH
Confidence             1123446677788888765443

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=96.93  E-value=0.066  Score=46.51  Aligned_cols=94  Identities=13%  Similarity=0.107  Sum_probs=57.6

Q ss_pred             CceEEEEEeCCCCc--hhHHHhhccCCCCCCCceEEEEecc-hhHHhh-cCCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCF--SQLESLMGSLDWLTPVSRIILTTRN-KQVLRN-WGVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~iivTtR~-~~~~~~-~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +++-++|+|+++..  ..+..+...+-.....+.+|++|.. ..+... .+....+.+.+++.++....+...+-...  
T Consensus       117 g~~KV~IIDEa~~LT~~A~NALLKtLEEPP~~tifILaTte~~KLl~TI~SRcq~ieF~~L~~eeI~~~L~~il~keg--  194 (725)
T PRK07133        117 SKYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIFILATTEVHKIPLTILSRVQRFNFRRISEDEIVSRLEFILEKEN--  194 (725)
T ss_pred             CCCEEEEEEChhhCCHHHHHHHHHHhhcCCCceEEEEEcCChhhhhHHHHhhceeEEccCCCHHHHHHHHHHHHHHcC--
Confidence            45568999999855  3467776665554445555555543 333322 24457899999999998887776542211  


Q ss_pred             CccHHHHHHHHHHHhCCCch
Q 039644          143 DVGYEKLSSNVTKYAQGIPL  162 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Pl  162 (192)
                      -....+.+..+++.++|.+.
T Consensus       195 I~id~eAl~~LA~lS~GslR  214 (725)
T PRK07133        195 ISYEKNALKLIAKLSSGSLR  214 (725)
T ss_pred             CCCCHHHHHHHHHHcCCCHH
Confidence            11123445667777777654

>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=96.92  E-value=0.012  Score=39.35  Aligned_cols=15  Identities=40%  Similarity=0.603  Sum_probs=13.8

Q ss_pred             CchhHHHHHHHHHhh
Q 039644            1 IGKTAIARAIFDKIS   15 (192)
Q Consensus         1 iGKTtLa~~~~~~~~   15 (192)
                      +|||++|+.+++.+.
T Consensus         9 ~GKT~l~~~la~~l~   23 (132)
T PF00004_consen    9 TGKTTLARALAQYLG   23 (132)
T ss_dssp             SSHHHHHHHHHHHTT
T ss_pred             CCeeHHHHHHHhhcc
Confidence            699999999999985

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 ....

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

Probab=96.91  E-value=0.013  Score=45.33  Aligned_cols=88  Identities=13%  Similarity=0.164  Sum_probs=59.2

Q ss_pred             EEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchhHHhhc--CCCceEecCCCCHHHHHHHHHHhhcCCCCCCccH
Q 039644           71 LIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQVLRNW--GVSKIYEMEALEYHHALELFSQHAFKRNHPDVGY  146 (192)
Q Consensus        71 LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~~~~~~--~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~  146 (192)
                      .+|||+++++.  .|..+...+.+....+++++.+.........  +....+..++|..++...-++..+....  -+-.
T Consensus       132 iiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcnylsrii~pi~SRC~KfrFk~L~d~~iv~rL~~Ia~~E~--v~~d  209 (346)
T KOG0989|consen  132 IIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSRIIRPLVSRCQKFRFKKLKDEDIVDRLEKIASKEG--VDID  209 (346)
T ss_pred             EEEEechhhhhHHHHHHHHHHHhccccceEEEEEcCChhhCChHHHhhHHHhcCCCcchHHHHHHHHHHHHHhC--CCCC
Confidence            79999999774  4888877777667777777776553322111  3345688999999998888888764322  2233


Q ss_pred             HHHHHHHHHHhCCC
Q 039644          147 EKLSSNVTKYAQGI  160 (192)
Q Consensus       147 ~~~~~~i~~~~~g~  160 (192)
                      ++..+.|++.++|.
T Consensus       210 ~~al~~I~~~S~Gd  223 (346)
T KOG0989|consen  210 DDALKLIAKISDGD  223 (346)
T ss_pred             HHHHHHHHHHcCCc
Confidence            45566677777665

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=96.90  E-value=0.014  Score=44.57  Aligned_cols=69  Identities=7%  Similarity=0.089  Sum_probs=40.5

Q ss_pred             EEEEEeCCCCc----------hhHHHhhccCCCCCCCceEEEEecchhHHh--------hcCCCceEecCCCCHHHHHHH
Q 039644           70 VLIVFDDVTCF----------SQLESLMGSLDWLTPVSRIILTTRNKQVLR--------NWGVSKIYEMEALEYHHALEL  131 (192)
Q Consensus        70 ~LlVlDdv~~~----------~~~~~l~~~~~~~~~~~~iivTtR~~~~~~--------~~~~~~~~~l~~l~~~ea~~l  131 (192)
                      .+|++|+++..          ...+.+...+........+++++.......        .......+.+++++.++..++
T Consensus       107 ~VL~IDE~~~L~~~~~~~~~~~~i~~Ll~~~e~~~~~~~vila~~~~~~~~~~~~~p~L~sRf~~~i~f~~~~~~el~~I  186 (261)
T TIGR02881       107 GVLFIDEAYSLARGGEKDFGKEAIDTLVKGMEDNRNEFVLILAGYSDEMDYFLSLNPGLRSRFPISIDFPDYTVEELMEI  186 (261)
T ss_pred             CEEEEechhhhccCCccchHHHHHHHHHHHHhccCCCEEEEecCCcchhHHHHhcChHHHhccceEEEECCCCHHHHHHH
Confidence            58999999752          234445444444333444555543322110        011235688999999999999


Q ss_pred             HHHhhcC
Q 039644          132 FSQHAFK  138 (192)
Q Consensus       132 f~~~~~~  138 (192)
                      +.+.+..
T Consensus       187 l~~~~~~  193 (261)
T TIGR02881       187 AERMVKE  193 (261)
T ss_pred             HHHHHHH
Confidence            9877643

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.

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=96.83  E-value=0.077  Score=45.06  Aligned_cols=95  Identities=12%  Similarity=0.111  Sum_probs=57.1

Q ss_pred             CceEEEEEeCCCCc--hhHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCF--SQLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      ++.-++|+|+++..  ..+..+...+......+.+|++|.... +...+ +....+...+++.++....+...+-.... 
T Consensus       118 ~~~kViIIDE~~~Lt~~a~naLLKtLEepp~~~ifIlatt~~~ki~~tI~SRc~~~~f~~~~~~ei~~~L~~i~~~egi-  196 (559)
T PRK05563        118 AKYKVYIIDEVHMLSTGAFNALLKTLEEPPAHVIFILATTEPHKIPATILSRCQRFDFKRISVEDIVERLKYILDKEGI-  196 (559)
T ss_pred             CCeEEEEEECcccCCHHHHHHHHHHhcCCCCCeEEEEEeCChhhCcHHHHhHheEEecCCCCHHHHHHHHHHHHHHcCC-
Confidence            45568899999865  346777666655444555665554332 22221 34567889999999988888775532221 


Q ss_pred             CccHHHHHHHHHHHhCCCchH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Pla  163 (192)
                       ....+....|++.++|.+..
T Consensus       197 -~i~~~al~~ia~~s~G~~R~  216 (559)
T PRK05563        197 -EYEDEALRLIARAAEGGMRD  216 (559)
T ss_pred             -CCCHHHHHHHHHHcCCCHHH
Confidence             11234455666667666543

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=96.81  E-value=0.024  Score=44.31  Aligned_cols=66  Identities=12%  Similarity=0.215  Sum_probs=38.6

Q ss_pred             ceEEEEEeCCCCc--hh-HHHhhccCCCCCCCceEEEEecchhHHhh-c-CCCceEecCCCCHHHHHHHHH
Q 039644           68 MKVLIVFDDVTCF--SQ-LESLMGSLDWLTPVSRIILTTRNKQVLRN-W-GVSKIYEMEALEYHHALELFS  133 (192)
Q Consensus        68 ~~~LlVlDdv~~~--~~-~~~l~~~~~~~~~~~~iivTtR~~~~~~~-~-~~~~~~~l~~l~~~ea~~lf~  133 (192)
                      .+-++|+|+++..  .. ...+...+.....++++|+||........ . +....+.++..+.++..+++.
T Consensus       100 ~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n~~~~l~~~l~sR~~~i~~~~p~~~~~~~il~  170 (316)
T PHA02544        100 GGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITANNKNGIIEPLRSRCRVIDFGVPTKEEQIEMMK  170 (316)
T ss_pred             CCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcCChhhchHHHHhhceEEEeCCCCHHHHHHHHH
Confidence            4568999999855  22 23333323334567788888865432111 1 334567777778777766544

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

Probab=96.80  E-value=0.0067  Score=46.44  Aligned_cols=78  Identities=15%  Similarity=0.137  Sum_probs=48.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHh--------cCCCC--cC------chHHHHhh
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNIL--------KDKNV--MP------YIDLNFRR   64 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~--------~~~~~--~~------~~~~l~~~   64 (192)
                      +|||+|+.++++.++.+|...+++..+++..   ..+.++...+...-.        ...++  ..      ..-.+.++
T Consensus        80 ~GKTtLa~~i~~~i~~~~~~~~V~~~iGer~---~Ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~~~~~a~~~AEy  156 (274)
T cd01133          80 VGKTVLIMELINNIAKAHGGYSVFAGVGERT---REGNDLYHEMKESGVLSKTALVYGQMNEPPGARARVALTGLTMAEY  156 (274)
T ss_pred             CChhHHHHHHHHHHHhcCCCEEEEEEeccCc---HHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHHHHHHHHHH
Confidence            5999999999999887887777766554421   345666666544211        01111  00      22223444


Q ss_pred             c---CCceEEEEEeCCCCch
Q 039644           65 L---SRMKVLIVFDDVTCFS   81 (192)
Q Consensus        65 l---~~~~~LlVlDdv~~~~   81 (192)
                      +   .+++.|+++||+....
T Consensus       157 fr~~~g~~Vl~~~Dsltr~a  176 (274)
T cd01133         157 FRDEEGQDVLLFIDNIFRFT  176 (274)
T ss_pred             HHHhcCCeEEEEEeChhHHH
Confidence            4   3789999999997554

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.

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=96.77  E-value=0.034  Score=47.72  Aligned_cols=111  Identities=13%  Similarity=0.019  Sum_probs=61.3

Q ss_pred             chHHHHhhcCCceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEE--EecchhHHhh-c-CCCceEecCCCCHHHHHH
Q 039644           57 YIDLNFRRLSRMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIIL--TTRNKQVLRN-W-GVSKIYEMEALEYHHALE  130 (192)
Q Consensus        57 ~~~~l~~~l~~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iiv--TtR~~~~~~~-~-~~~~~~~l~~l~~~ea~~  130 (192)
                      .+..+...+.+++++++-|+.|...  .|+.+...+....+...+++  ||++...... . +....+.+.+++.++...
T Consensus       281 ~Q~~Ll~~Le~~~v~~~~~~~~~~~~~~~~~ik~~~~~~~~~~~VLI~aTt~~~~~l~~aLrSR~~~i~~~pls~edi~~  360 (615)
T TIGR02903       281 LQNKLLKVLEDKRVEFSSSYYDPDDPNVPKYIKKLFEEGAPADFVLIGATTRDPEEINPALRSRCAEVFFEPLTPEDIAL  360 (615)
T ss_pred             HHHHHHHHHhhCeEEeecceeccCCcccchhhhhhcccCccceEEEEEeccccccccCHHHHhceeEEEeCCCCHHHHHH
Confidence            4566777777777777766665432  35555544444334444444  4554331111 1 233567899999999999


Q ss_pred             HHHHhhcCCCCCCccHHHHHHHHHHHhCCCchHHHHHHH
Q 039644          131 LFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSC  169 (192)
Q Consensus       131 lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plai~~~~~  169 (192)
                      ++...+.....  .-..+....|.+.+..-+.|+..++.
T Consensus       361 Il~~~a~~~~v--~ls~eal~~L~~ys~~gRraln~L~~  397 (615)
T TIGR02903       361 IVLNAAEKINV--HLAAGVEELIARYTIEGRKAVNILAD  397 (615)
T ss_pred             HHHHHHHHcCC--CCCHHHHHHHHHCCCcHHHHHHHHHH
Confidence            99987643211  11233344444444444566665543

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.

>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=96.75  E-value=0.023  Score=42.24  Aligned_cols=69  Identities=16%  Similarity=0.076  Sum_probs=41.9

Q ss_pred             eEEEEecchhHHhhc--CCCceEecCCCCHHHHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCCchHHHHHH
Q 039644           98 RIILTTRNKQVLRNW--GVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLS  168 (192)
Q Consensus        98 ~iivTtR~~~~~~~~--~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plai~~~~  168 (192)
                      -|=-|||.-.+..+.  ...-..+++..+.+|-..+..+.+..-+  -+...+.+.+|++.+.|-|.-..-+-
T Consensus       152 ligATTr~g~ls~pLrdRFgi~~~l~~Y~~~el~~Iv~r~a~~l~--i~i~~~~~~~Ia~rsrGtPRiAnrll  222 (233)
T PF05496_consen  152 LIGATTRAGLLSSPLRDRFGIVLRLEFYSEEELAKIVKRSARILN--IEIDEDAAEEIARRSRGTPRIANRLL  222 (233)
T ss_dssp             EEEEESSGCCTSHCCCTTSSEEEE----THHHHHHHHHHCCHCTT---EE-HHHHHHHHHCTTTSHHHHHHHH
T ss_pred             EeeeeccccccchhHHhhcceecchhcCCHHHHHHHHHHHHHHhC--CCcCHHHHHHHHHhcCCChHHHHHHH
Confidence            344577765444443  2234567999999999999988764332  34456778899999999996444333

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.

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=96.74  E-value=0.044  Score=44.35  Aligned_cols=91  Identities=21%  Similarity=0.330  Sum_probs=51.7

Q ss_pred             CceEEEEEeCCCCch------------h----HHHhhccCCCC--CCCceEEEEecchhHHhhc-----CCCceEecCCC
Q 039644           67 RMKVLIVFDDVTCFS------------Q----LESLMGSLDWL--TPVSRIILTTRNKQVLRNW-----GVSKIYEMEAL  123 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~------------~----~~~l~~~~~~~--~~~~~iivTtR~~~~~~~~-----~~~~~~~l~~l  123 (192)
                      ..+.+|+||+++...            .    +..+...+...  ..+..||.||.........     .....+.++..
T Consensus       223 ~~p~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~~~~~~~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P  302 (389)
T PRK03992        223 KAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLP  302 (389)
T ss_pred             cCCeEEEEechhhhhcccccCCCCccHHHHHHHHHHHHhccccCCCCCEEEEEecCChhhCCHHHcCCccCceEEEECCC
Confidence            467899999997531            1    12222222221  2355677777654322211     12457889999


Q ss_pred             CHHHHHHHHHHhhcCCCCC-CccHHHHHHHHHHHhCCCc
Q 039644          124 EYHHALELFSQHAFKRNHP-DVGYEKLSSNVTKYAQGIP  161 (192)
Q Consensus       124 ~~~ea~~lf~~~~~~~~~~-~~~~~~~~~~i~~~~~g~P  161 (192)
                      +.++-.++|..+......+ ...    ...+++.+.|+-
T Consensus       303 ~~~~R~~Il~~~~~~~~~~~~~~----~~~la~~t~g~s  337 (389)
T PRK03992        303 DEEGRLEILKIHTRKMNLADDVD----LEELAELTEGAS  337 (389)
T ss_pred             CHHHHHHHHHHHhccCCCCCcCC----HHHHHHHcCCCC
Confidence            9999999998876433221 122    345666666654

>PRK08181 transposase; Validated

Probab=96.69  E-value=0.0069  Score=46.40  Aligned_cols=89  Identities=20%  Similarity=0.132  Sum_probs=45.8

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||.||..+++....+...++|+.           ..+++..+......  .   ....+...+. +.-||||||+...
T Consensus       117 tGKTHLa~Aia~~a~~~g~~v~f~~-----------~~~L~~~l~~a~~~--~---~~~~~l~~l~-~~dLLIIDDlg~~  179 (269)
T PRK08181        117 GGKSHLAAAIGLALIENGWRVLFTR-----------TTDLVQKLQVARRE--L---QLESAIAKLD-KFDLLILDDLAYV  179 (269)
T ss_pred             CcHHHHHHHHHHHHHHcCCceeeee-----------HHHHHHHHHHHHhC--C---cHHHHHHHHh-cCCEEEEeccccc
Confidence            6999999999997655544455554           34455444332211  1   1112222222 3349999999633


Q ss_pred             --hhH--HHhhccCCCCCCCceEEEEecch
Q 039644           81 --SQL--ESLMGSLDWLTPVSRIILTTRNK  106 (192)
Q Consensus        81 --~~~--~~l~~~~~~~~~~~~iivTtR~~  106 (192)
                        ..+  ..+...+...-.+..+||||...
T Consensus       180 ~~~~~~~~~Lf~lin~R~~~~s~IiTSN~~  209 (269)
T PRK08181        180 TKDQAETSVLFELISARYERRSILITANQP  209 (269)
T ss_pred             cCCHHHHHHHHHHHHHHHhCCCEEEEcCCC
Confidence              111  12222222111123588888764

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=96.69  E-value=0.22  Score=39.24  Aligned_cols=91  Identities=15%  Similarity=0.230  Sum_probs=62.7

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +..=++|+|+++...  ..+.+...+-+-..++.+|++|.+.. +...+ +....+.+.+++.+++.+.+....   .  
T Consensus       107 ~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTI~SRCq~~~~~~~~~~~~~~~L~~~~---~--  181 (319)
T PRK06090        107 NGYRLFVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHNQKRLLPTIVSRCQQWVVTPPSTAQAMQWLKGQG---I--  181 (319)
T ss_pred             CCceEEEecchhhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhcceeEeCCCCCHHHHHHHHHHcC---C--
Confidence            345589999999764  46777776666667788888777654 33333 556789999999999988876531   1  


Q ss_pred             CccHHHHHHHHHHHhCCCchHHHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLALKVL  167 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai~~~  167 (192)
                      +     ....++..++|.|+...-+
T Consensus       182 ~-----~~~~~l~l~~G~p~~A~~~  201 (319)
T PRK06090        182 T-----VPAYALKLNMGSPLKTLAM  201 (319)
T ss_pred             c-----hHHHHHHHcCCCHHHHHHH
Confidence            1     1245678899999865443

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=96.66  E-value=0.18  Score=39.68  Aligned_cols=94  Identities=15%  Similarity=0.164  Sum_probs=60.0

Q ss_pred             CceEEEEEeCCCCchh--HHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFSQ--LESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~~--~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +.+-++|+|+++....  .+.+...+-... .+.+|++|.+.. +...+ +....+++.+++.++..+.+........  
T Consensus       123 ~~~kVvII~~ae~m~~~aaNaLLK~LEEPp-~~~fILi~~~~~~Ll~TI~SRcq~i~f~~l~~~~~~~~L~~~~~~~~--  199 (314)
T PRK07399        123 APRKVVVIEDAETMNEAAANALLKTLEEPG-NGTLILIAPSPESLLPTIVSRCQIIPFYRLSDEQLEQVLKRLGDEEI--  199 (314)
T ss_pred             CCceEEEEEchhhcCHHHHHHHHHHHhCCC-CCeEEEEECChHhCcHHHHhhceEEecCCCCHHHHHHHHHHhhcccc--
Confidence            4566999999986643  566665555444 455666665543 22222 5568899999999999999887642111  


Q ss_pred             CccHHHHHHHHHHHhCCCchHHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLALKV  166 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai~~  166 (192)
                         .......++..++|.|..+..
T Consensus       200 ---~~~~~~~l~~~a~Gs~~~al~  220 (314)
T PRK07399        200 ---LNINFPELLALAQGSPGAAIA  220 (314)
T ss_pred             ---chhHHHHHHHHcCCCHHHHHH
Confidence               111134678888888865443

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=96.65  E-value=0.055  Score=41.86  Aligned_cols=69  Identities=10%  Similarity=0.044  Sum_probs=41.8

Q ss_pred             eEEEEEeCCCCc-----------hhHHHhhccCCCCCCCceEEEEecchhHHhh--c------CCCceEecCCCCHHHHH
Q 039644           69 KVLIVFDDVTCF-----------SQLESLMGSLDWLTPVSRIILTTRNKQVLRN--W------GVSKIYEMEALEYHHAL  129 (192)
Q Consensus        69 ~~LlVlDdv~~~-----------~~~~~l~~~~~~~~~~~~iivTtR~~~~~~~--~------~~~~~~~l~~l~~~ea~  129 (192)
                      .-+|+||++...           ...+.+...+.....+.+||.++........  .      .....+.+++++.+|..
T Consensus       122 ~gvL~iDEi~~L~~~~~~~~~~~~~~~~Ll~~le~~~~~~~vI~a~~~~~~~~~~~~np~L~sR~~~~i~fp~l~~edl~  201 (284)
T TIGR02880       122 GGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENQRDDLVVILAGYKDRMDSFFESNPGFSSRVAHHVDFPDYSEAELL  201 (284)
T ss_pred             CcEEEEechhhhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHHHhhCHHHHhhCCcEEEeCCcCHHHHH
Confidence            368999999732           1234455444444455566666543221111  0      12456899999999999


Q ss_pred             HHHHHhhc
Q 039644          130 ELFSQHAF  137 (192)
Q Consensus       130 ~lf~~~~~  137 (192)
                      .++....-
T Consensus       202 ~I~~~~l~  209 (284)
T TIGR02880       202 VIAGLMLK  209 (284)
T ss_pred             HHHHHHHH
Confidence            99887653

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.

>COG3899 Predicted ATPase [General function prediction only]

Probab=96.63  E-value=0.04  Score=49.00  Aligned_cols=104  Identities=14%  Similarity=0.154  Sum_probs=63.9

Q ss_pred             CceEEEEEeCCCC-----chhHHHhhccCCCCC-CCceEEE--Eecch--hHHhhcCCCceEecCCCCHHHHHHHHHHhh
Q 039644           67 RMKVLIVFDDVTC-----FSQLESLMGSLDWLT-PVSRIIL--TTRNK--QVLRNWGVSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus        67 ~~~~LlVlDdv~~-----~~~~~~l~~~~~~~~-~~~~iiv--TtR~~--~~~~~~~~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      .++.++|+||+.-     .+-++.+........ ..+.|..  |.+..  .+.......+.+.|.||+..+...+.....
T Consensus       153 ~~plVi~leDlhWaD~~SL~lL~~lm~~~~~~~~~~n~v~~~h~~~~~~~~~~~~~~~i~~I~L~PL~~~d~~~lV~~~l  232 (849)
T COG3899         153 EHPLVIVLEDLHWADSASLKLLQLLMDRIAIGAYRDNEVLLLHPLRPTLGEILKSATNITTITLAPLSRADTNQLVAATL  232 (849)
T ss_pred             cCCeEEEEecccccChhHHHHHHHHHHhcchhhhhccccccCCCccchhhHHhhcCCceeEEecCcCchhhHHHHHHHHh
Confidence            4699999999952     122344433332000 0112222  22222  122222345789999999999999998876


Q ss_pred             cCCCCCCccHHHHHHHHHHHhCCCchHHHHHHHHhcc
Q 039644          137 FKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHK  173 (192)
Q Consensus       137 ~~~~~~~~~~~~~~~~i~~~~~g~Plai~~~~~~l~~  173 (192)
                      ....   ....+....|+++..|+|+=+.-+-..|..
T Consensus       233 ~~~~---~~~~p~~~~i~~kt~GnPfFi~e~lk~l~~  266 (849)
T COG3899         233 GCTK---LLPAPLLELIFEKTKGNPFFIEEFLKALYE  266 (849)
T ss_pred             CCcc---cccchHHHHHHHHhcCCCccHHHHHHHHHh
Confidence            4422   234456778999999999988887776655

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=96.61  E-value=0.25  Score=39.00  Aligned_cols=89  Identities=12%  Similarity=0.166  Sum_probs=60.9

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +++=++|+|+++...  ....+...+-+-..++.+|++|.+.. +...+ +....+.+.+++.+++.+.+......  . 
T Consensus       106 g~~KV~iI~~a~~m~~~AaNaLLKtLEEPp~~~~fiL~t~~~~~llpTI~SRC~~~~~~~~~~~~~~~~L~~~~~~--~-  182 (325)
T PRK06871        106 GGNKVVYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADLSAALLPTIYSRCQTWLIHPPEEQQALDWLQAQSSA--E-  182 (325)
T ss_pred             CCceEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhCchHHHhhceEEeCCCCCHHHHHHHHHHHhcc--C-
Confidence            455688999999765  36677776766667778888887654 22222 45678999999999998888765311  1 


Q ss_pred             CccHHHHHHHHHHHhCCCch
Q 039644          143 DVGYEKLSSNVTKYAQGIPL  162 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Pl  162 (192)
                          ...+...+..++|.|+
T Consensus       183 ----~~~~~~~~~l~~g~p~  198 (325)
T PRK06871        183 ----ISEILTALRINYGRPL  198 (325)
T ss_pred             ----hHHHHHHHHHcCCCHH
Confidence                1124456777888886

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=96.57  E-value=0.17  Score=40.07  Aligned_cols=90  Identities=13%  Similarity=0.139  Sum_probs=61.6

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +.+=++|+|+++.+.  ....+...+-+-..++.+|++|.+.. +...+ +....+.+.+++.+++.+.+....+  .  
T Consensus       107 g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTIrSRCq~~~~~~~~~~~~~~~L~~~~~--~--  182 (334)
T PRK07993        107 GGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATLRSRCRLHYLAPPPEQYALTWLSREVT--M--  182 (334)
T ss_pred             CCceEEEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhccccccCCCCCHHHHHHHHHHccC--C--
Confidence            456689999999765  36777776766667788888887654 33232 4456789999999998887754321  1  


Q ss_pred             CccHHHHHHHHHHHhCCCchH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Pla  163 (192)
                         ..+.+..++..++|.|..
T Consensus       183 ---~~~~a~~~~~la~G~~~~  200 (334)
T PRK07993        183 ---SQDALLAALRLSAGAPGA  200 (334)
T ss_pred             ---CHHHHHHHHHHcCCCHHH
Confidence               122355678889999863

>CHL00176 ftsH cell division protein; Validated

Probab=96.55  E-value=0.1  Score=44.98  Aligned_cols=97  Identities=11%  Similarity=0.195  Sum_probs=53.6

Q ss_pred             HHhhcCCceEEEEEeCCCCch------------h----HHHhhccCCCC--CCCceEEEEecchhHHhhc-----CCCce
Q 039644           61 NFRRLSRMKVLIVFDDVTCFS------------Q----LESLMGSLDWL--TPVSRIILTTRNKQVLRNW-----GVSKI  117 (192)
Q Consensus        61 l~~~l~~~~~LlVlDdv~~~~------------~----~~~l~~~~~~~--~~~~~iivTtR~~~~~~~~-----~~~~~  117 (192)
                      +.......+++|+||+++...            .    +..+...+...  ..+..||.+|.........     .....
T Consensus       268 F~~A~~~~P~ILfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~~~~~ViVIaaTN~~~~LD~ALlRpGRFd~~  347 (638)
T CHL00176        268 FKKAKENSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQ  347 (638)
T ss_pred             HHHHhcCCCcEEEEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhccccCCCCeeEEEecCchHhhhhhhhccccCceE
Confidence            333445678999999996431            1    23333333222  2344566666554322211     12467


Q ss_pred             EecCCCCHHHHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCC
Q 039644          118 YEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGI  160 (192)
Q Consensus       118 ~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~  160 (192)
                      +.++..+.++-.++++.+.....   .........+.+.+.|+
T Consensus       348 I~v~lPd~~~R~~IL~~~l~~~~---~~~d~~l~~lA~~t~G~  387 (638)
T CHL00176        348 ITVSLPDREGRLDILKVHARNKK---LSPDVSLELIARRTPGF  387 (638)
T ss_pred             EEECCCCHHHHHHHHHHHHhhcc---cchhHHHHHHHhcCCCC
Confidence            78888888888888887764321   11223345666666664

>CHL00181 cbbX CbbX; Provisional

Probab=96.52  E-value=0.16  Score=39.42  Aligned_cols=68  Identities=7%  Similarity=0.088  Sum_probs=42.1

Q ss_pred             EEEEEeCCCCc-----------hhHHHhhccCCCCCCCceEEEEecchhHHh--------hcCCCceEecCCCCHHHHHH
Q 039644           70 VLIVFDDVTCF-----------SQLESLMGSLDWLTPVSRIILTTRNKQVLR--------NWGVSKIYEMEALEYHHALE  130 (192)
Q Consensus        70 ~LlVlDdv~~~-----------~~~~~l~~~~~~~~~~~~iivTtR~~~~~~--------~~~~~~~~~l~~l~~~ea~~  130 (192)
                      -+|+||++...           ...+.+...+.....+..||.++....+..        .......+..++++.++..+
T Consensus       124 gVLfIDE~~~l~~~~~~~~~~~e~~~~L~~~me~~~~~~~vI~ag~~~~~~~~~~~np~L~sR~~~~i~F~~~t~~el~~  203 (287)
T CHL00181        124 GVLFIDEAYYLYKPDNERDYGSEAIEILLQVMENQRDDLVVIFAGYKDRMDKFYESNPGLSSRIANHVDFPDYTPEELLQ  203 (287)
T ss_pred             CEEEEEccchhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHHHhcCHHHHHhCCceEEcCCcCHHHHHH
Confidence            48999999742           123444444444445566666665333211        11234579999999999999


Q ss_pred             HHHHhhc
Q 039644          131 LFSQHAF  137 (192)
Q Consensus       131 lf~~~~~  137 (192)
                      ++...+-
T Consensus       204 I~~~~l~  210 (287)
T CHL00181        204 IAKIMLE  210 (287)
T ss_pred             HHHHHHH
Confidence            9887764

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=96.51  E-value=0.15  Score=40.34  Aligned_cols=69  Identities=17%  Similarity=0.225  Sum_probs=48.1

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHh
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQH  135 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~  135 (192)
                      +.+=++|+|+++...  ..+.+...+.+...++.+|++|.+.. +.... +....+++.+++.++..+.+...
T Consensus       109 ~~~kvviI~~a~~~~~~a~NaLLK~LEEPp~~~~~Il~t~~~~~ll~TIrSRc~~i~~~~~~~~~~~~~L~~~  181 (329)
T PRK08058        109 SNKKVYIIEHADKMTASAANSLLKFLEEPSGGTTAILLTENKHQILPTILSRCQVVEFRPLPPESLIQRLQEE  181 (329)
T ss_pred             cCceEEEeehHhhhCHHHHHHHHHHhcCCCCCceEEEEeCChHhCcHHHHhhceeeeCCCCCHHHHHHHHHHc
Confidence            345579999998654  36677777766667777888876644 22222 45678999999999987777643

>TIGR03689 pup_AAA proteasome ATPase

Probab=96.51  E-value=0.017  Score=48.24  Aligned_cols=70  Identities=17%  Similarity=0.273  Sum_probs=42.2

Q ss_pred             CceEEEEEeCCCCc---------hh-----HHHhhccCCCCC--CCceEEEEecchhHHhhc-----CCCceEecCCCCH
Q 039644           67 RMKVLIVFDDVTCF---------SQ-----LESLMGSLDWLT--PVSRIILTTRNKQVLRNW-----GVSKIYEMEALEY  125 (192)
Q Consensus        67 ~~~~LlVlDdv~~~---------~~-----~~~l~~~~~~~~--~~~~iivTtR~~~~~~~~-----~~~~~~~l~~l~~  125 (192)
                      +.+++|+||+++..         .+     ...+...+....  .+..||.||.........     .....+.++..+.
T Consensus       288 g~p~IIfIDEiD~L~~~R~~~~s~d~e~~il~~LL~~LDgl~~~~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~  367 (512)
T TIGR03689       288 GRPVIVFFDEMDSIFRTRGSGVSSDVETTVVPQLLSELDGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDA  367 (512)
T ss_pred             CCCceEEEehhhhhhcccCCCccchHHHHHHHHHHHHhcccccCCceEEEeccCChhhCCHhhcCccccceEEEeCCCCH
Confidence            46899999999742         11     223433333222  334455566554332211     1245689999999


Q ss_pred             HHHHHHHHHhh
Q 039644          126 HHALELFSQHA  136 (192)
Q Consensus       126 ~ea~~lf~~~~  136 (192)
                      ++..++|..+.
T Consensus       368 e~r~~Il~~~l  378 (512)
T TIGR03689       368 EAAADIFSKYL  378 (512)
T ss_pred             HHHHHHHHHHh
Confidence            99999998875

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.

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=96.46  E-value=0.008  Score=42.26  Aligned_cols=118  Identities=17%  Similarity=0.094  Sum_probs=58.0

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHh----cC------CCCcC-------chHHHHh
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNIL----KD------KNVMP-------YIDLNFR   63 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~----~~------~~~~~-------~~~~l~~   63 (192)
                      .||||+|...+-+...+=..+.++..+... .. ..-..+++.+- .+.    +.      .+..+       ..+..++
T Consensus        13 ~Gkt~~a~g~~~ra~~~g~~v~~vQFlKg~-~~-~gE~~~l~~l~-~v~~~~~g~~~~~~~~~~~~~~~~a~~~~~~a~~   89 (159)
T cd00561          13 KGKTTAALGLALRALGHGYRVGVVQFLKGG-WK-YGELKALERLP-NIEIHRMGRGFFWTTENDEEDIAAAAEGWAFAKE   89 (159)
T ss_pred             CCHHHHHHHHHHHHHHCCCeEEEEEEeCCC-Cc-cCHHHHHHhCC-CcEEEECCCCCccCCCChHHHHHHHHHHHHHHHH
Confidence            499999999999754443344444333321 00 22223332220 000    00      00001       3334444


Q ss_pred             hcCCceE-EEEEeCCCCc-----hhHHHhhccCCCCCCCceEEEEecchhHHhhcCCCceEecC
Q 039644           64 RLSRMKV-LIVFDDVTCF-----SQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEME  121 (192)
Q Consensus        64 ~l~~~~~-LlVlDdv~~~-----~~~~~l~~~~~~~~~~~~iivTtR~~~~~~~~~~~~~~~l~  121 (192)
                      .+....| |+|||.+..-     -..+.+...+.....+..+|+|.|+..-.-..-...+.+|.
T Consensus        90 ~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p~~l~e~AD~VTEm~  153 (159)
T cd00561          90 AIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAPKELIEAADLVTEMR  153 (159)
T ss_pred             HHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCCHHHHHhCceeeecc
Confidence            5555444 9999999532     12344444444444567899999986533332233344443

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.

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

Probab=96.44  E-value=0.059  Score=43.75  Aligned_cols=94  Identities=18%  Similarity=0.244  Sum_probs=52.7

Q ss_pred             CCceEEEEEeCCCCch------------h----HHHhhccCCC--CCCCceEEEEecchhHHhhc-----CCCceEecCC
Q 039644           66 SRMKVLIVFDDVTCFS------------Q----LESLMGSLDW--LTPVSRIILTTRNKQVLRNW-----GVSKIYEMEA  122 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~~------------~----~~~l~~~~~~--~~~~~~iivTtR~~~~~~~~-----~~~~~~~l~~  122 (192)
                      ...+++|+||+++...            .    +..+...+..  ...+..||.||.........     .....+.++.
T Consensus       236 ~~~P~ILfIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~~ld~~~~~~~v~VI~aTN~~d~LDpAllR~GRfd~~I~~~~  315 (398)
T PTZ00454        236 ENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPL  315 (398)
T ss_pred             hcCCeEEEEECHhhhccccccccCCccHHHHHHHHHHHHHhhccCCCCCEEEEEecCCchhCCHHHcCCCcccEEEEeCC
Confidence            4578999999986320            1    2233332322  12455678888765433221     2245688888


Q ss_pred             CCHHHHHHHHHHhhcCCC-CCCccHHHHHHHHHHHhCCCchH
Q 039644          123 LEYHHALELFSQHAFKRN-HPDVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       123 l~~~ea~~lf~~~~~~~~-~~~~~~~~~~~~i~~~~~g~Pla  163 (192)
                      .+.++...+|........ .++..    ...+++.+.|+.-|
T Consensus       316 P~~~~R~~Il~~~~~~~~l~~dvd----~~~la~~t~g~sga  353 (398)
T PTZ00454        316 PDRRQKRLIFQTITSKMNLSEEVD----LEDFVSRPEKISAA  353 (398)
T ss_pred             cCHHHHHHHHHHHHhcCCCCcccC----HHHHHHHcCCCCHH
Confidence            888888888876653222 11222    34566667666444

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

Probab=96.43  E-value=0.16  Score=39.41  Aligned_cols=160  Identities=12%  Similarity=0.100  Sum_probs=87.6

Q ss_pred             CchhHHHHHHHHHhhCCCc------ceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-cC---chHHHHhhcCC-ce
Q 039644            1 IGKTAIARAIFDKISGDFE------CSCFLENVREESQRPGGLACLRQKLLSNILKDKNV-MP---YIDLNFRRLSR-MK   69 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~------~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~---~~~~l~~~l~~-~~   69 (192)
                      +|||++++.++......++      .++.+. ..+    .++...++..|+..++..... ..   ......+.++. +-
T Consensus        72 nGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq-~P~----~p~~~~~Y~~IL~~lgaP~~~~~~~~~~~~~~~~llr~~~v  146 (302)
T PF05621_consen   72 NGKTMIIERFRRLHPPQSDEDAERIPVVYVQ-MPP----EPDERRFYSAILEALGAPYRPRDRVAKLEQQVLRLLRRLGV  146 (302)
T ss_pred             CcHHHHHHHHHHHCCCCCCCCCccccEEEEe-cCC----CCChHHHHHHHHHHhCcccCCCCCHHHHHHHHHHHHHHcCC
Confidence            5999999999986544443      233333 222    279999999999999866544 22   23333445543 45


Q ss_pred             EEEEEeCCCCch-----hHHHhhc---cCCCCCCCceEEEEecchhHHhhc-----CCCceEecCCCCHHHHH-HHHHHh
Q 039644           70 VLIVFDDVTCFS-----QLESLMG---SLDWLTPVSRIILTTRNKQVLRNW-----GVSKIYEMEALEYHHAL-ELFSQH  135 (192)
Q Consensus        70 ~LlVlDdv~~~~-----~~~~l~~---~~~~~~~~~~iivTtR~~~~~~~~-----~~~~~~~l~~l~~~ea~-~lf~~~  135 (192)
                      -+||+|.+.+.-     +-..+..   .+-+.-.-+-|.+-|+.-.-+...     +....+.++....++-. .|+...
T Consensus       147 rmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~vGt~~A~~al~~D~QLa~RF~~~~Lp~W~~d~ef~~LL~s~  226 (302)
T PF05621_consen  147 RMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVGVGTREAYRALRTDPQLASRFEPFELPRWELDEEFRRLLASF  226 (302)
T ss_pred             cEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEEeccHHHHHHhccCHHHHhccCCccCCCCCCCcHHHHHHHHH
Confidence            689999997531     1112211   122222334455555442222111     12345667766655433 333221


Q ss_pred             h---cCCCCCCccHHHHHHHHHHHhCCCchHHH
Q 039644          136 A---FKRNHPDVGYEKLSSNVTKYAQGIPLALK  165 (192)
Q Consensus       136 ~---~~~~~~~~~~~~~~~~i~~~~~g~Plai~  165 (192)
                      .   .-.....-...+++..|...++|+.=-+.
T Consensus       227 e~~LPLr~~S~l~~~~la~~i~~~s~G~iG~l~  259 (302)
T PF05621_consen  227 ERALPLRKPSNLASPELARRIHERSEGLIGELS  259 (302)
T ss_pred             HHhCCCCCCCCCCCHHHHHHHHHHcCCchHHHH
Confidence            1   11112234456788999999999865443

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

>PRK12608 transcription termination factor Rho; Provisional

Probab=96.32  E-value=0.019  Score=45.84  Aligned_cols=75  Identities=21%  Similarity=0.315  Sum_probs=47.9

Q ss_pred             CchhHHHHHHHHHhhCCC-cce-EEEeeccccccCCCChHHHHHHHHHHHhcCCCC---cC------chHHHHhhc--CC
Q 039644            1 IGKTAIARAIFDKISGDF-ECS-CFLENVREESQRPGGLACLRQKLLSNILKDKNV---MP------YIDLNFRRL--SR   67 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F-~~~-~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---~~------~~~~l~~~l--~~   67 (192)
                      +|||||++.+++.+.... +.. +|+. +.+   .+..+.++...+...+.....+   ..      ....+.+++  .+
T Consensus       144 tGKTTLl~~la~~i~~~~~dv~~vv~l-IgE---R~~EV~df~~~i~~~Vvast~de~~~~~~~v~~~~~~~Ae~f~~~G  219 (380)
T PRK12608        144 AGKTVLLQQIAAAVAANHPEVHLMVLL-IDE---RPEEVTDMRRSVKGEVYASTFDRPPDEHIRVAELVLERAKRLVEQG  219 (380)
T ss_pred             CCHHHHHHHHHHHHHhcCCCceEEEEE-ecC---CCCCHHHHHHHHhhhEEeecCCCCHHHHHHHHHHHHHHHHHHHHcC
Confidence            699999999999876544 333 3433 322   2367889998888776654322   11      222233333  47


Q ss_pred             ceEEEEEeCCCC
Q 039644           68 MKVLIVFDDVTC   79 (192)
Q Consensus        68 ~~~LlVlDdv~~   79 (192)
                      ++.+||+|++..
T Consensus       220 kdVVLvlDsltr  231 (380)
T PRK12608        220 KDVVILLDSLTR  231 (380)
T ss_pred             CCEEEEEeCcHH
Confidence            899999999953

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=96.28  E-value=0.099  Score=43.73  Aligned_cols=93  Identities=15%  Similarity=0.208  Sum_probs=49.8

Q ss_pred             CCceEEEEEeCCCCch------------h----HHHhhccCCCC--CCCceEEEEecchhHHhh-----cCCCceEecCC
Q 039644           66 SRMKVLIVFDDVTCFS------------Q----LESLMGSLDWL--TPVSRIILTTRNKQVLRN-----WGVSKIYEMEA  122 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~~------------~----~~~l~~~~~~~--~~~~~iivTtR~~~~~~~-----~~~~~~~~l~~  122 (192)
                      ...+++|+||+++...            .    ...+...+...  ..+..||.||........     ......+.++.
T Consensus       145 ~~~p~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~~~~v~vI~aTn~~~~ld~al~r~gRfd~~i~i~~  224 (495)
T TIGR01241       145 KNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDL  224 (495)
T ss_pred             hcCCCEEEEechhhhhhccccCcCCccHHHHHHHHHHHhhhccccCCCCeEEEEecCChhhcCHHHhcCCcceEEEEcCC
Confidence            4567899999996421            1    12232222221  233445556655431111     12346788888


Q ss_pred             CCHHHHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCCc
Q 039644          123 LEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIP  161 (192)
Q Consensus       123 l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  161 (192)
                      .+.++-.++|..+....... .  ......+++.+.|+-
T Consensus       225 Pd~~~R~~il~~~l~~~~~~-~--~~~l~~la~~t~G~s  260 (495)
T TIGR01241       225 PDIKGREEILKVHAKNKKLA-P--DVDLKAVARRTPGFS  260 (495)
T ss_pred             CCHHHHHHHHHHHHhcCCCC-c--chhHHHHHHhCCCCC
Confidence            88888888888765332211 1  112346777777654

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.

>PRK12377 putative replication protein; Provisional

Probab=96.24  E-value=0.024  Score=42.92  Aligned_cols=89  Identities=16%  Similarity=0.129  Sum_probs=46.7

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCC-
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTC-   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~-   79 (192)
                      +|||+||..+++.+......++++.           ..+++..+-...... .   ....+.+.+ .+.-||||||+.. 
T Consensus       112 tGKThLa~AIa~~l~~~g~~v~~i~-----------~~~l~~~l~~~~~~~-~---~~~~~l~~l-~~~dLLiIDDlg~~  175 (248)
T PRK12377        112 TGKNHLAAAIGNRLLAKGRSVIVVT-----------VPDVMSRLHESYDNG-Q---SGEKFLQEL-CKVDLLVLDEIGIQ  175 (248)
T ss_pred             CCHHHHHHHHHHHHHHcCCCeEEEE-----------HHHHHHHHHHHHhcc-c---hHHHHHHHh-cCCCEEEEcCCCCC
Confidence            6999999999998766555556664           334444443333211 1   111223333 3455899999942 


Q ss_pred             -chhHH--HhhccCCC-CCCCceEEEEecc
Q 039644           80 -FSQLE--SLMGSLDW-LTPVSRIILTTRN  105 (192)
Q Consensus        80 -~~~~~--~l~~~~~~-~~~~~~iivTtR~  105 (192)
                       ...|.  .+...+.. .....-+|+||..
T Consensus       176 ~~s~~~~~~l~~ii~~R~~~~~ptiitSNl  205 (248)
T PRK12377        176 RETKNEQVVLNQIIDRRTASMRSVGMLTNL  205 (248)
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCEEEEcCC
Confidence             22332  22222221 1223347778764

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=96.14  E-value=0.26  Score=39.16  Aligned_cols=88  Identities=15%  Similarity=0.179  Sum_probs=58.8

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      ++.-++|+|+++...  ..+.+...+-+-..++.+|++|.+.. +...+ +....+.+.+++.++..+.+....   .. 
T Consensus       131 ~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~LLpTI~SRcq~i~~~~~~~~~~~~~L~~~~---~~-  206 (342)
T PRK06964        131 GGARVVVLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARIDRLLPTILSRCRQFPMTVPAPEAAAAWLAAQG---VA-  206 (342)
T ss_pred             CCceEEEEechhhcCHHHHHHHHHHhcCCCcCcEEEEEECChhhCcHHHHhcCEEEEecCCCHHHHHHHHHHcC---CC-
Confidence            345589999999764  47777777776667777777776644 33232 455789999999999998886641   11 


Q ss_pred             CccHHHHHHHHHHHhCCCchHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLAL  164 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai  164 (192)
                       +     ...++..++|.|+..
T Consensus       207 -~-----~~~~l~~~~Gsp~~A  222 (342)
T PRK06964        207 -D-----ADALLAEAGGAPLAA  222 (342)
T ss_pred             -h-----HHHHHHHcCCCHHHH
Confidence             1     123466778888643

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

Probab=96.11  E-value=0.35  Score=42.57  Aligned_cols=76  Identities=11%  Similarity=0.168  Sum_probs=38.6

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-c--CchHHHHhhcCCce-EEEEEeC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV-M--PYIDLNFRRLSRMK-VLIVFDD   76 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~--~~~~~l~~~l~~~~-~LlVlDd   76 (192)
                      +|||+||+.++..+..   ..+.++ +++.... ....        .+.+..+. .  +....+.+.++.++ .+++||+
T Consensus       495 vGKT~lA~~la~~l~~---~~~~~d-~se~~~~-~~~~--------~lig~~~gyvg~~~~~~l~~~~~~~p~~VvllDE  561 (731)
T TIGR02639       495 VGKTELAKQLAEALGV---HLERFD-MSEYMEK-HTVS--------RLIGAPPGYVGFEQGGLLTEAVRKHPHCVLLLDE  561 (731)
T ss_pred             ccHHHHHHHHHHHhcC---CeEEEe-Cchhhhc-ccHH--------HHhcCCCCCcccchhhHHHHHHHhCCCeEEEEec
Confidence            6999999999997732   234444 3332111 1111        12222221 1  12223444444444 5999999


Q ss_pred             CCCch--hHHHhhcc
Q 039644           77 VTCFS--QLESLMGS   89 (192)
Q Consensus        77 v~~~~--~~~~l~~~   89 (192)
                      ++..+  .++.|...
T Consensus       562 ieka~~~~~~~Ll~~  576 (731)
T TIGR02639       562 IEKAHPDIYNILLQV  576 (731)
T ss_pred             hhhcCHHHHHHHHHh
Confidence            98543  34444443

>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=96.11  E-value=0.071  Score=37.63  Aligned_cols=58  Identities=17%  Similarity=0.235  Sum_probs=35.4

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchhH-Hhhc-CCCceEecCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQV-LRNW-GVSKIYEMEALE  124 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~~-~~~~-~~~~~~~l~~l~  124 (192)
                      +..=++|||+++...  ....++..+-....++.+|++|++... .... +....+.+.+++
T Consensus       101 ~~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~fiL~t~~~~~il~TI~SRc~~i~~~~ls  162 (162)
T PF13177_consen  101 GKYKVIIIDEADKLTEEAQNALLKTLEEPPENTYFILITNNPSKILPTIRSRCQVIRFRPLS  162 (162)
T ss_dssp             SSSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEEEEEES-GGGS-HHHHTTSEEEEE----
T ss_pred             CCceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEEEEEECChHHChHHHHhhceEEecCCCC
Confidence            345689999999764  366776666666678899999887653 2222 555667776653

...

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

Probab=96.11  E-value=0.05  Score=44.66  Aligned_cols=117  Identities=19%  Similarity=0.221  Sum_probs=62.7

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHH-HHhhcCCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDL-NFRRLSRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~-l~~~l~~~~~LlVlDdv~~   79 (192)
                      +|||++|+.+++.....|-   .+. .+.          +..    ...+..  ...+.. +.......+++|+||+++.
T Consensus       228 TGKT~LAraIA~el~~~fi---~V~-~se----------L~~----k~~Ge~--~~~vr~lF~~A~~~~P~ILfIDEID~  287 (438)
T PTZ00361        228 TGKTLLAKAVANETSATFL---RVV-GSE----------LIQ----KYLGDG--PKLVRELFRVAEENAPSIVFIDEIDA  287 (438)
T ss_pred             CCHHHHHHHHHHhhCCCEE---EEe-cch----------hhh----hhcchH--HHHHHHHHHHHHhCCCcEEeHHHHHH
Confidence            6999999999998765542   221 111          110    000000  001111 2222245688999999753


Q ss_pred             ch------------h----HHHhhccCCC--CCCCceEEEEecchhHHhhc-----CCCceEecCCCCHHHHHHHHHHhh
Q 039644           80 FS------------Q----LESLMGSLDW--LTPVSRIILTTRNKQVLRNW-----GVSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus        80 ~~------------~----~~~l~~~~~~--~~~~~~iivTtR~~~~~~~~-----~~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      ..            .    +-.+...+..  ...+..||.+|.........     .....+.++..+..+..++|..+.
T Consensus       288 l~~kR~~~~sgg~~e~qr~ll~LL~~Ldg~~~~~~V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~~  367 (438)
T PTZ00361        288 IGTKRYDATSGGEKEIQRTMLELLNQLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHT  367 (438)
T ss_pred             HhccCCCCCCcccHHHHHHHHHHHHHHhhhcccCCeEEEEecCChHHhhHHhccCCeeEEEEEeCCCCHHHHHHHHHHHH
Confidence            21            0    1122222221  12356788888765443332     124578899999999999998775


Q ss_pred             c
Q 039644          137 F  137 (192)
Q Consensus       137 ~  137 (192)
                      .
T Consensus       368 ~  368 (438)
T PTZ00361        368 S  368 (438)
T ss_pred             h
Confidence            3

>PRK09183 transposase/IS protein; Provisional

Probab=96.09  E-value=0.025  Score=43.14  Aligned_cols=24  Identities=25%  Similarity=0.065  Sum_probs=16.0

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEE
Q 039644            1 IGKTAIARAIFDKISGDFECSCFL   24 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv   24 (192)
                      +|||+||..++......-..+.++
T Consensus       113 tGKThLa~al~~~a~~~G~~v~~~  136 (259)
T PRK09183        113 VGKTHLAIALGYEAVRAGIKVRFT  136 (259)
T ss_pred             CCHHHHHHHHHHHHHHcCCeEEEE
Confidence            699999999988644332233344

>PRK06921 hypothetical protein; Provisional

Probab=95.97  E-value=0.019  Score=44.03  Aligned_cols=25  Identities=16%  Similarity=0.117  Sum_probs=19.2

Q ss_pred             CchhHHHHHHHHHhhCC-CcceEEEe
Q 039644            1 IGKTAIARAIFDKISGD-FECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~-F~~~~wv~   25 (192)
                      +|||.||..+++.+..+ ...++|+.
T Consensus       128 ~GKThLa~aia~~l~~~~g~~v~y~~  153 (266)
T PRK06921        128 SGKTHLLTAAANELMRKKGVPVLYFP  153 (266)
T ss_pred             CcHHHHHHHHHHHHhhhcCceEEEEE
Confidence            69999999999987654 44556665

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=95.92  E-value=0.22  Score=41.67  Aligned_cols=67  Identities=15%  Similarity=0.262  Sum_probs=47.3

Q ss_pred             EEEEEeCCC--CchhHHHhhccCCCCCCCceEEEEecchhHHhh--cCCCceEecCCCCHHHHHHHHHHhh
Q 039644           70 VLIVFDDVT--CFSQLESLMGSLDWLTPVSRIILTTRNKQVLRN--WGVSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus        70 ~LlVlDdv~--~~~~~~~l~~~~~~~~~~~~iivTtR~~~~~~~--~~~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      =++|+|.|+  +.+.|..+...+-.-....++|..|.+.+-...  .+..+.+.++.++.++....+...+
T Consensus       121 KVyiIDEvHMLS~~afNALLKTLEEPP~hV~FIlATTe~~Kip~TIlSRcq~f~fkri~~~~I~~~L~~i~  191 (515)
T COG2812         121 KVYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQKIPNTILSRCQRFDFKRLDLEEIAKHLAAIL  191 (515)
T ss_pred             eEEEEecHHhhhHHHHHHHhcccccCccCeEEEEecCCcCcCchhhhhccccccccCCCHHHHHHHHHHHH
Confidence            389999998  456689988887765666666666665442222  2556789999999988777766654

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=95.88  E-value=0.045  Score=36.49  Aligned_cols=25  Identities=24%  Similarity=0.351  Sum_probs=18.8

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +||||+++.++..+.......+++.
T Consensus        13 ~GKTtl~~~l~~~~~~~~~~~~~~~   37 (148)
T smart00382       13 SGKTTLARALARELGPPGGGVIYID   37 (148)
T ss_pred             CcHHHHHHHHHhccCCCCCCEEEEC
Confidence            6999999999998765544455554

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.

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

Probab=95.84  E-value=0.12  Score=44.52  Aligned_cols=62  Identities=23%  Similarity=0.239  Sum_probs=37.7

Q ss_pred             CchhHHHHHHHHHhhC-CCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCC
Q 039644            1 IGKTAIARAIFDKISG-DFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVT   78 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~-~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~   78 (192)
                      +|||+||+++++++.. .+-.+.+++ .+..  ....+..+++.+-             ..+..++.-.+.++||||++
T Consensus       442 sGKT~L~kal~~~~~k~~~~hv~~v~-Cs~l--~~~~~e~iQk~l~-------------~vfse~~~~~PSiIvLDdld  504 (952)
T KOG0735|consen  442 SGKTNLVKALFDYYSKDLIAHVEIVS-CSTL--DGSSLEKIQKFLN-------------NVFSEALWYAPSIIVLDDLD  504 (952)
T ss_pred             CCHhHHHHHHHHHhccccceEEEEEe-chhc--cchhHHHHHHHHH-------------HHHHHHHhhCCcEEEEcchh
Confidence            6999999999997653 333344444 2221  1123444443332             22455667789999999996

>PRK06835 DNA replication protein DnaC; Validated

Probab=95.69  E-value=0.029  Score=44.32  Aligned_cols=90  Identities=16%  Similarity=0.197  Sum_probs=45.1

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||.||..+++.+...-..++++.           ..+++..+.........  +... ....+.+ -=||||||+...
T Consensus       194 tGKThLa~aIa~~l~~~g~~V~y~t-----------~~~l~~~l~~~~~~~~~--~~~~-~~~~l~~-~DLLIIDDlG~e  258 (329)
T PRK06835        194 TGKTFLSNCIAKELLDRGKSVIYRT-----------ADELIEILREIRFNNDK--ELEE-VYDLLIN-CDLLIIDDLGTE  258 (329)
T ss_pred             CcHHHHHHHHHHHHHHCCCeEEEEE-----------HHHHHHHHHHHHhccch--hHHH-HHHHhcc-CCEEEEeccCCC
Confidence            6999999999998654444556664           33444333322111111  1111 1222222 238999999533


Q ss_pred             --hhH--HHhhccCCC-CCCCceEEEEecc
Q 039644           81 --SQL--ESLMGSLDW-LTPVSRIILTTRN  105 (192)
Q Consensus        81 --~~~--~~l~~~~~~-~~~~~~iivTtR~  105 (192)
                        ..|  +.+...+.. ...+..+||||..
T Consensus       259 ~~t~~~~~~Lf~iin~R~~~~k~tIiTSNl  288 (329)
T PRK06835        259 KITEFSKSELFNLINKRLLRQKKMIISTNL  288 (329)
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCCEEEECCC
Confidence              222  223222221 1234568888865

>PRK06526 transposase; Provisional

Probab=95.67  E-value=0.026  Score=42.91  Aligned_cols=88  Identities=16%  Similarity=0.102  Sum_probs=42.9

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||+||..++......-..+.|+           ...++...+...... +.   ....+. .+. +.-||||||+...
T Consensus       109 tGKThLa~al~~~a~~~g~~v~f~-----------t~~~l~~~l~~~~~~-~~---~~~~l~-~l~-~~dlLIIDD~g~~  171 (254)
T PRK06526        109 TGKTHLAIGLGIRACQAGHRVLFA-----------TAAQWVARLAAAHHA-GR---LQAELV-KLG-RYPLLIVDEVGYI  171 (254)
T ss_pred             CchHHHHHHHHHHHHHCCCchhhh-----------hHHHHHHHHHHHHhc-Cc---HHHHHH-Hhc-cCCEEEEcccccC
Confidence            699999999998754332233333           233444444332211 11   112222 222 3458999999743


Q ss_pred             h--h-H-HHhhccCCC-CCCCceEEEEecch
Q 039644           81 S--Q-L-ESLMGSLDW-LTPVSRIILTTRNK  106 (192)
Q Consensus        81 ~--~-~-~~l~~~~~~-~~~~~~iivTtR~~  106 (192)
                      .  . . +.+...+.. ...++ +|+||...
T Consensus       172 ~~~~~~~~~L~~li~~r~~~~s-~IitSn~~  201 (254)
T PRK06526        172 PFEPEAANLFFQLVSSRYERAS-LIVTSNKP  201 (254)
T ss_pred             CCCHHHHHHHHHHHHHHHhcCC-EEEEcCCC
Confidence            1  1 1 122222211 12233 88888764

>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=95.66  E-value=0.043  Score=41.26  Aligned_cols=25  Identities=16%  Similarity=0.388  Sum_probs=21.6

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +|||+|+..+.......|+.++++.
T Consensus        24 SGKT~li~~lL~~~~~~f~~I~l~t   48 (241)
T PF04665_consen   24 SGKTTLIKSLLYYLRHKFDHIFLIT   48 (241)
T ss_pred             CCHHHHHHHHHHhhcccCCEEEEEe
Confidence            6999999999999999997776664

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

>PRK08939 primosomal protein DnaI; Reviewed

Probab=95.53  E-value=0.067  Score=41.84  Aligned_cols=88  Identities=15%  Similarity=0.206  Sum_probs=47.5

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCC-
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTC-   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~-   79 (192)
                      +|||.||..+++.+...-..+.++.           ..+++..+-......     ........+. +.=||||||+-. 
T Consensus       167 ~GKThLa~Aia~~l~~~g~~v~~~~-----------~~~l~~~lk~~~~~~-----~~~~~l~~l~-~~dlLiIDDiG~e  229 (306)
T PRK08939        167 VGKSYLLAAIANELAKKGVSSTLLH-----------FPEFIRELKNSISDG-----SVKEKIDAVK-EAPVLMLDDIGAE  229 (306)
T ss_pred             CCHHHHHHHHHHHHHHcCCCEEEEE-----------HHHHHHHHHHHHhcC-----cHHHHHHHhc-CCCEEEEecCCCc
Confidence            6999999999998654433445554           334444544443221     1122223333 345899999963 


Q ss_pred             -chhHHH--hhccCCC-C-CCCceEEEEecc
Q 039644           80 -FSQLES--LMGSLDW-L-TPVSRIILTTRN  105 (192)
Q Consensus        80 -~~~~~~--l~~~~~~-~-~~~~~iivTtR~  105 (192)
                       ...|..  +...+.+ . ..+...|+||..
T Consensus       230 ~~s~~~~~~ll~~Il~~R~~~~~~ti~TSNl  260 (306)
T PRK08939        230 QMSSWVRDEVLGVILQYRMQEELPTFFTSNF  260 (306)
T ss_pred             cccHHHHHHHHHHHHHHHHHCCCeEEEECCC
Confidence             344542  3333321 1 234457777753

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=95.53  E-value=0.76  Score=34.87  Aligned_cols=163  Identities=15%  Similarity=0.133  Sum_probs=88.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-cC-----chHHHHhhc-CCce-EEE
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV-MP-----YIDLNFRRL-SRMK-VLI   72 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~-----~~~~l~~~l-~~~~-~Ll   72 (192)
                      +|||.+++.+.....+.=.+++.++  .+.    .....+...+..++..+..- ..     ....+.... ++++ ..+
T Consensus        62 sGKTv~~Ral~~s~~~d~~~~v~i~--~~~----~s~~~~~~ai~~~l~~~p~~~~~~~~e~~~~~L~al~~~g~r~v~l  135 (269)
T COG3267          62 SGKTVLRRALLASLNEDQVAVVVID--KPT----LSDATLLEAIVADLESQPKVNVNAVLEQIDRELAALVKKGKRPVVL  135 (269)
T ss_pred             CchhHHHHHHHHhcCCCceEEEEec--Ccc----hhHHHHHHHHHHHhccCccchhHHHHHHHHHHHHHHHHhCCCCeEE
Confidence            5999999955555443322333332  221    45666777777777663322 22     223333333 4555 899


Q ss_pred             EEeCCCCch--h---HHHhhccCCCCCCCceEEEEe--------cchhHHhhcCCCce-EecCCCCHHHHHHHHHHhhcC
Q 039644           73 VFDDVTCFS--Q---LESLMGSLDWLTPVSRIILTT--------RNKQVLRNWGVSKI-YEMEALEYHHALELFSQHAFK  138 (192)
Q Consensus        73 VlDdv~~~~--~---~~~l~~~~~~~~~~~~iivTt--------R~~~~~~~~~~~~~-~~l~~l~~~ea~~lf~~~~~~  138 (192)
                      +.|+.....  .   ...|...-..+..--+|+..-        |............. |++.|++..+....++.+..+
T Consensus       136 ~vdEah~L~~~~le~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~lr~~~l~e~~~R~~ir~~l~P~~~~~t~~yl~~~Le~  215 (269)
T COG3267         136 MVDEAHDLNDSALEALRLLTNLEEDSSKLLSIVLIGQPKLRPRLRLPVLRELEQRIDIRIELPPLTEAETGLYLRHRLEG  215 (269)
T ss_pred             eehhHhhhChhHHHHHHHHHhhcccccCceeeeecCCcccchhhchHHHHhhhheEEEEEecCCcChHHHHHHHHHHHhc
Confidence            999997542  2   233333222222112233321        11111111112233 899999999888777766544


Q ss_pred             CCCC-CccHHHHHHHHHHHhCCCchHHHHHHH
Q 039644          139 RNHP-DVGYEKLSSNVTKYAQGIPLALKVLSC  169 (192)
Q Consensus       139 ~~~~-~~~~~~~~~~i~~~~~g~Plai~~~~~  169 (192)
                      ...+ +---++....|.....|.|.+|..++.
T Consensus       216 a~~~~~l~~~~a~~~i~~~sqg~P~lin~~~~  247 (269)
T COG3267         216 AGLPEPLFSDDALLLIHEASQGIPRLINNLAT  247 (269)
T ss_pred             cCCCcccCChhHHHHHHHHhccchHHHHHHHH
Confidence            3322 222345566788889999999988774

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=95.45  E-value=0.42  Score=37.77  Aligned_cols=68  Identities=13%  Similarity=0.141  Sum_probs=41.5

Q ss_pred             ceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchhHHh-hc-CCCceEecCCCCHHHHHHHHHHh
Q 039644           68 MKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQVLR-NW-GVSKIYEMEALEYHHALELFSQH  135 (192)
Q Consensus        68 ~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~~~~-~~-~~~~~~~l~~l~~~ea~~lf~~~  135 (192)
                      .+-++|+|+++..+  ....+...+.....++.+|++|.+..... .. +....+.+.+++.+++.+.+...
T Consensus       113 ~~kV~iiEp~~~Ld~~a~naLLk~LEep~~~~~~Ilvth~~~~ll~ti~SRc~~~~~~~~~~~~~~~~L~~~  184 (325)
T PRK08699        113 GLRVILIHPAESMNLQAANSLLKVLEEPPPQVVFLLVSHAADKVLPTIKSRCRKMVLPAPSHEEALAYLRER  184 (325)
T ss_pred             CceEEEEechhhCCHHHHHHHHHHHHhCcCCCEEEEEeCChHhChHHHHHHhhhhcCCCCCHHHHHHHHHhc
Confidence            34455678887653  23444333333334566888887755222 22 44577899999999988877553

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=95.40  E-value=0.13  Score=45.11  Aligned_cols=137  Identities=17%  Similarity=0.252  Sum_probs=69.8

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhh-cCCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRR-LSRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~-l~~~~~LlVlDdv~~   79 (192)
                      +|||+||+.+++.....|   +.+.           ..++..    ...+..  ...+..+... -...+++|+||+++.
T Consensus       498 tGKT~lakalA~e~~~~f---i~v~-----------~~~l~~----~~vGes--e~~i~~~f~~A~~~~p~iifiDEid~  557 (733)
T TIGR01243       498 TGKTLLAKAVATESGANF---IAVR-----------GPEILS----KWVGES--EKAIREIFRKARQAAPAIIFFDEIDA  557 (733)
T ss_pred             CCHHHHHHHHHHhcCCCE---EEEe-----------hHHHhh----cccCcH--HHHHHHHHHHHHhcCCEEEEEEChhh
Confidence            699999999999876543   1121           111111    110100  0122222222 245689999999963


Q ss_pred             ch--------------hHHHhhccCCCC--CCCceEEEEecchhHHhhc-----CCCceEecCCCCHHHHHHHHHHhhcC
Q 039644           80 FS--------------QLESLMGSLDWL--TPVSRIILTTRNKQVLRNW-----GVSKIYEMEALEYHHALELFSQHAFK  138 (192)
Q Consensus        80 ~~--------------~~~~l~~~~~~~--~~~~~iivTtR~~~~~~~~-----~~~~~~~l~~l~~~ea~~lf~~~~~~  138 (192)
                      ..              ....+...+...  ..+.-||.||.........     .....+.++..+.++-.++|+.+...
T Consensus       558 l~~~r~~~~~~~~~~~~~~~lL~~ldg~~~~~~v~vI~aTn~~~~ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~~  637 (733)
T TIGR01243       558 IAPARGARFDTSVTDRIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRS  637 (733)
T ss_pred             hhccCCCCCCccHHHHHHHHHHHHhhcccCCCCEEEEEeCCChhhCCHhhcCCCccceEEEeCCcCHHHHHHHHHHHhcC
Confidence            21              123333333321  2333455566554432221     23567888888888888888766532


Q ss_pred             CCC-CCccHHHHHHHHHHHhCCCc
Q 039644          139 RNH-PDVGYEKLSSNVTKYAQGIP  161 (192)
Q Consensus       139 ~~~-~~~~~~~~~~~i~~~~~g~P  161 (192)
                      ... ++..    ...+++.+.|+-
T Consensus       638 ~~~~~~~~----l~~la~~t~g~s  657 (733)
T TIGR01243       638 MPLAEDVD----LEELAEMTEGYT  657 (733)
T ss_pred             CCCCccCC----HHHHHHHcCCCC
Confidence            221 1222    334556666654

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.

>PRK07952 DNA replication protein DnaC; Validated

Probab=95.40  E-value=0.089  Score=39.77  Aligned_cols=90  Identities=17%  Similarity=0.165  Sum_probs=47.7

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||+||..+++.+...-..+++++           ..+++..+-........   ....+...+.. .=||||||+...
T Consensus       110 tGKThLa~aia~~l~~~g~~v~~it-----------~~~l~~~l~~~~~~~~~---~~~~~l~~l~~-~dlLvIDDig~~  174 (244)
T PRK07952        110 TGKNHLAAAICNELLLRGKSVLIIT-----------VADIMSAMKDTFSNSET---SEEQLLNDLSN-VDLLVIDEIGVQ  174 (244)
T ss_pred             CCHHHHHHHHHHHHHhcCCeEEEEE-----------HHHHHHHHHHHHhhccc---cHHHHHHHhcc-CCEEEEeCCCCC
Confidence            6999999999998755544455553           34555444433321111   22234444543 347888999643


Q ss_pred             --hhHHH--hhccCCC-CCCCceEEEEecc
Q 039644           81 --SQLES--LMGSLDW-LTPVSRIILTTRN  105 (192)
Q Consensus        81 --~~~~~--l~~~~~~-~~~~~~iivTtR~  105 (192)
                        .+|+.  +...+.. ......+||||..
T Consensus       175 ~~s~~~~~~l~~Ii~~Ry~~~~~tiitSNl  204 (244)
T PRK07952        175 TESRYEKVIINQIVDRRSSSKRPTGMLTNS  204 (244)
T ss_pred             CCCHHHHHHHHHHHHHHHhCCCCEEEeCCC
Confidence              33432  2111111 1223457777764

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

Probab=95.31  E-value=0.84  Score=36.44  Aligned_cols=147  Identities=18%  Similarity=0.291  Sum_probs=82.8

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCC-ceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSR-MKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~-~~~LlVlDdv~~   79 (192)
                      .|||-||++|+++....|     +.+++.             ++.+...+.+..  +++.++...+. .+++|.+|.++.
T Consensus       196 TGKTLLAkAVA~~T~AtF-----IrvvgS-------------ElVqKYiGEGaR--lVRelF~lArekaPsIIFiDEIDA  255 (406)
T COG1222         196 TGKTLLAKAVANQTDATF-----IRVVGS-------------ELVQKYIGEGAR--LVRELFELAREKAPSIIFIDEIDA  255 (406)
T ss_pred             CcHHHHHHHHHhccCceE-----EEeccH-------------HHHHHHhccchH--HHHHHHHHHhhcCCeEEEEechhh
Confidence            599999999999887643     443332             333343343332  55556666654 599999999963


Q ss_pred             ch------------h----HHHhhccCCCCC--CCceEEEEecchhHHhhc-----CCCceEecCCCCHHHHHHHHHHhh
Q 039644           80 FS------------Q----LESLMGSLDWLT--PVSRIILTTRNKQVLRNW-----GVSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus        80 ~~------------~----~~~l~~~~~~~~--~~~~iivTtR~~~~~~~~-----~~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      ..            +    +=++...+..+.  .+-|||..|.-.+...+.     ...+.++.+.-+.+--.++|.-++
T Consensus       256 Ig~kR~d~~t~gDrEVQRTmleLL~qlDGFD~~~nvKVI~ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHt  335 (406)
T COG1222         256 IGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHT  335 (406)
T ss_pred             hhcccccCCCCchHHHHHHHHHHHHhccCCCCCCCeEEEEecCCccccChhhcCCCcccceeecCCCCHHHHHHHHHHHh
Confidence            21            1    223444444433  456888887665544433     224567777444444556676665


Q ss_pred             cCCC-CCCccHHHHHHHHHHHhCCCch----HHHHHHHHh
Q 039644          137 FKRN-HPDVGYEKLSSNVTKYAQGIPL----ALKVLSCFL  171 (192)
Q Consensus       137 ~~~~-~~~~~~~~~~~~i~~~~~g~Pl----ai~~~~~~l  171 (192)
                      ..=+ .++-.++    .+++.+.|.-=    |+-+=||.+
T Consensus       336 rkM~l~~dvd~e----~la~~~~g~sGAdlkaictEAGm~  371 (406)
T COG1222         336 RKMNLADDVDLE----LLARLTEGFSGADLKAICTEAGMF  371 (406)
T ss_pred             hhccCccCcCHH----HHHHhcCCCchHHHHHHHHHHhHH
Confidence            3222 2233344    56666776643    344445543

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=95.24  E-value=0.049  Score=48.50  Aligned_cols=15  Identities=33%  Similarity=0.432  Sum_probs=13.0

Q ss_pred             CchhHHHHHHHHHhh
Q 039644            1 IGKTAIARAIFDKIS   15 (192)
Q Consensus         1 iGKTtLa~~~~~~~~   15 (192)
                      +|||.||+.++..+-
T Consensus       607 vGKT~lA~~La~~l~  621 (852)
T TIGR03345       607 VGKTETALALAELLY  621 (852)
T ss_pred             CCHHHHHHHHHHHHh
Confidence            699999999998763

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.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=95.23  E-value=0.076  Score=47.21  Aligned_cols=80  Identities=14%  Similarity=0.191  Sum_probs=40.7

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-cC--chHHHHhhcCCce-EEEEEeC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV-MP--YIDLNFRRLSRMK-VLIVFDD   76 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~--~~~~l~~~l~~~~-~LlVlDd   76 (192)
                      +|||+||+.+++.+-..-...+-++ +++.... .....        +.+..+. ..  ....+...++.++ .+++||+
T Consensus       550 vGKt~lA~~LA~~l~~~~~~~~~~d-~s~~~~~-~~~~~--------l~g~~~gyvg~~~~~~l~~~~~~~p~~VvllDe  619 (821)
T CHL00095        550 VGKTELTKALASYFFGSEDAMIRLD-MSEYMEK-HTVSK--------LIGSPPGYVGYNEGGQLTEAVRKKPYTVVLFDE  619 (821)
T ss_pred             CcHHHHHHHHHHHhcCCccceEEEE-chhcccc-ccHHH--------hcCCCCcccCcCccchHHHHHHhCCCeEEEECC
Confidence            6999999999997533222333333 3332111 11222        1122222 21  2234555565565 4899999


Q ss_pred             CCCch--hHHHhhccC
Q 039644           77 VTCFS--QLESLMGSL   90 (192)
Q Consensus        77 v~~~~--~~~~l~~~~   90 (192)
                      ++..+  .++.|...+
T Consensus       620 ieka~~~v~~~Llq~l  635 (821)
T CHL00095        620 IEKAHPDIFNLLLQIL  635 (821)
T ss_pred             hhhCCHHHHHHHHHHh
Confidence            98543  345444433

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

Probab=95.22  E-value=0.31  Score=40.82  Aligned_cols=149  Identities=17%  Similarity=0.144  Sum_probs=78.5

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||+||..++..-  .|+.+=-+   |+.......-..-...             +...+....+..-..||+||+...
T Consensus       549 sGKTaLAA~iA~~S--~FPFvKii---Spe~miG~sEsaKc~~-------------i~k~F~DAYkS~lsiivvDdiErL  610 (744)
T KOG0741|consen  549 SGKTALAAKIALSS--DFPFVKII---SPEDMIGLSESAKCAH-------------IKKIFEDAYKSPLSIIVVDDIERL  610 (744)
T ss_pred             CChHHHHHHHHhhc--CCCeEEEe---ChHHccCccHHHHHHH-------------HHHHHHHhhcCcceEEEEcchhhh
Confidence            69999999998753  56653333   2211110111111111             111122223445568999999766


Q ss_pred             hhHHHh---------------hccCCCCCCCceEEEEecchhHHhhcC----CCceEecCCCCH-HHHHHHHHHhhcCCC
Q 039644           81 SQLESL---------------MGSLDWLTPVSRIILTTRNKQVLRNWG----VSKIYEMEALEY-HHALELFSQHAFKRN  140 (192)
Q Consensus        81 ~~~~~l---------------~~~~~~~~~~~~iivTtR~~~~~~~~~----~~~~~~l~~l~~-~ea~~lf~~~~~~~~  140 (192)
                      -+|..+               ....|+.+..-=|+-||....+...++    ....+.++.++. ++..+++...-   .
T Consensus       611 iD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~i~~~F~~~i~Vpnl~~~~~~~~vl~~~n---~  687 (744)
T KOG0741|consen  611 LDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMGILDCFSSTIHVPNLTTGEQLLEVLEELN---I  687 (744)
T ss_pred             hcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcCHHHhhhheeecCccCchHHHHHHHHHcc---C
Confidence            554322               222333333333444777777777773    256788898887 66777765542   1


Q ss_pred             CCCccHHHHHHHHHHHhCCCchHHHHHHHHhc
Q 039644          141 HPDVGYEKLSSNVTKYAQGIPLALKVLSCFLH  172 (192)
Q Consensus       141 ~~~~~~~~~~~~i~~~~~g~Plai~~~~~~l~  172 (192)
                      ..+...+..+.+...+|  +-..|+-+..++.
T Consensus       688 fsd~~~~~~~~~~~~~~--~~vgIKklL~lie  717 (744)
T KOG0741|consen  688 FSDDEVRAIAEQLLSKK--VNVGIKKLLMLIE  717 (744)
T ss_pred             CCcchhHHHHHHHhccc--cchhHHHHHHHHH
Confidence            22334555555665555  4444555555553

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=95.20  E-value=0.096  Score=46.77  Aligned_cols=95  Identities=18%  Similarity=0.191  Sum_probs=46.7

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-cC--chHHHHhhcCCce-EEEEEeC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV-MP--YIDLNFRRLSRMK-VLIVFDD   76 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~--~~~~l~~~l~~~~-~LlVlDd   76 (192)
                      +|||++|+.++..+...-...+.++ ++..... .        ....+.+..+. ..  ....+...++.++ .+++||+
T Consensus       606 vGKt~lA~~La~~l~~~~~~~i~~d-~s~~~~~-~--------~~~~l~g~~~g~~g~~~~g~l~~~v~~~p~~vlllDe  675 (852)
T TIGR03346       606 VGKTELAKALAEFLFDDEDAMVRID-MSEYMEK-H--------SVARLIGAPPGYVGYEEGGQLTEAVRRKPYSVVLFDE  675 (852)
T ss_pred             CCHHHHHHHHHHHhcCCCCcEEEEe-chhhccc-c--------hHHHhcCCCCCccCcccccHHHHHHHcCCCcEEEEec
Confidence            6999999999997543323333443 3332111 1        11222222222 21  1123333343333 4999999


Q ss_pred             CCCch--hHHHhhccCCCC-----------CCCceEEEEecc
Q 039644           77 VTCFS--QLESLMGSLDWL-----------TPVSRIILTTRN  105 (192)
Q Consensus        77 v~~~~--~~~~l~~~~~~~-----------~~~~~iivTtR~  105 (192)
                      +...+  .+..|...+..+           -.++-||+||..
T Consensus       676 ieka~~~v~~~Ll~~l~~g~l~d~~g~~vd~rn~iiI~TSn~  717 (852)
T TIGR03346       676 VEKAHPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNL  717 (852)
T ss_pred             cccCCHHHHHHHHHHHhcCceecCCCeEEecCCcEEEEeCCc
Confidence            98543  355554443221           123447777765

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.

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

Probab=95.15  E-value=0.061  Score=46.93  Aligned_cols=80  Identities=18%  Similarity=0.238  Sum_probs=47.6

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-cC--chHHHHhhcCCceE-EEEEeC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV-MP--YIDLNFRRLSRMKV-LIVFDD   76 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~--~~~~l~~~l~~~~~-LlVlDd   76 (192)
                      +|||.||+.++..+-..=...+-++ +|++...         .-+..+.+.++. ..  ---.|-+..+.+|| ++.||.
T Consensus       532 VGKTELAkaLA~~Lfg~e~aliR~D-MSEy~Ek---------HsVSrLIGaPPGYVGyeeGG~LTEaVRr~PySViLlDE  601 (786)
T COG0542         532 VGKTELAKALAEALFGDEQALIRID-MSEYMEK---------HSVSRLIGAPPGYVGYEEGGQLTEAVRRKPYSVILLDE  601 (786)
T ss_pred             ccHHHHHHHHHHHhcCCCccceeec-hHHHHHH---------HHHHHHhCCCCCCceeccccchhHhhhcCCCeEEEech
Confidence            7999999999997632223444444 4443222         334555566665 44  33445556677887 888899


Q ss_pred             CCCch--hHHHhhccC
Q 039644           77 VTCFS--QLESLMGSL   90 (192)
Q Consensus        77 v~~~~--~~~~l~~~~   90 (192)
                      +..-+  .++-|.+.+
T Consensus       602 IEKAHpdV~nilLQVl  617 (786)
T COG0542         602 IEKAHPDVFNLLLQVL  617 (786)
T ss_pred             hhhcCHHHHHHHHHHh
Confidence            97543  345444433

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

Probab=95.12  E-value=0.02  Score=41.08  Aligned_cols=62  Identities=24%  Similarity=0.268  Sum_probs=33.3

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~   79 (192)
                      +|||.||..+++....+-..+.|+.           ..+++..+-... . ..   ....+.+.+.+ .=||||||+-.
T Consensus        58 ~GKThLa~ai~~~~~~~g~~v~f~~-----------~~~L~~~l~~~~-~-~~---~~~~~~~~l~~-~dlLilDDlG~  119 (178)
T PF01695_consen   58 TGKTHLAVAIANEAIRKGYSVLFIT-----------ASDLLDELKQSR-S-DG---SYEELLKRLKR-VDLLILDDLGY  119 (178)
T ss_dssp             SSHHHHHHHHHHHHHHTT--EEEEE-----------HHHHHHHHHCCH-C-CT---THCHHHHHHHT-SSCEEEETCTS
T ss_pred             HHHHHHHHHHHHHhccCCcceeEee-----------cCceeccccccc-c-cc---chhhhcCcccc-ccEecccccce
Confidence            6999999999997544333456664           344554443221 1 11   11222333332 34788999964

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.

>CHL00195 ycf46 Ycf46; Provisional

Probab=94.91  E-value=0.13  Score=42.81  Aligned_cols=95  Identities=12%  Similarity=0.067  Sum_probs=49.7

Q ss_pred             CceEEEEEeCCCCch-------h-------HHHhhccCCCCCCCceEEEEecchhHHhh-----cCCCceEecCCCCHHH
Q 039644           67 RMKVLIVFDDVTCFS-------Q-------LESLMGSLDWLTPVSRIILTTRNKQVLRN-----WGVSKIYEMEALEYHH  127 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~-------~-------~~~l~~~~~~~~~~~~iivTtR~~~~~~~-----~~~~~~~~l~~l~~~e  127 (192)
                      ..+++|.||+++...       +       ...+...+.....+--||.||........     ......+.++.-+.++
T Consensus       317 ~~P~IL~IDEID~~~~~~~~~~d~~~~~rvl~~lL~~l~~~~~~V~vIaTTN~~~~Ld~allR~GRFD~~i~v~lP~~~e  396 (489)
T CHL00195        317 LSPCILWIDEIDKAFSNSESKGDSGTTNRVLATFITWLSEKKSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEE  396 (489)
T ss_pred             cCCcEEEehhhhhhhccccCCCCchHHHHHHHHHHHHHhcCCCceEEEEecCChhhCCHHHhCCCcCCeEEEeCCcCHHH
Confidence            468999999997321       0       12222222222233345556665432211     1234677888888888


Q ss_pred             HHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCCch
Q 039644          128 ALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPL  162 (192)
Q Consensus       128 a~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~Pl  162 (192)
                      -.++|..+...... ..........+++.+.|+-=
T Consensus       397 R~~Il~~~l~~~~~-~~~~~~dl~~La~~T~GfSG  430 (489)
T CHL00195        397 REKIFKIHLQKFRP-KSWKKYDIKKLSKLSNKFSG  430 (489)
T ss_pred             HHHHHHHHHhhcCC-CcccccCHHHHHhhcCCCCH
Confidence            88888877643221 10001123456666666643

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=94.67  E-value=0.21  Score=35.62  Aligned_cols=66  Identities=17%  Similarity=0.110  Sum_probs=37.2

Q ss_pred             chHHHHhhcCCceE-EEEEeCCCCch-----hHHHhhccCCCCCCCceEEEEecchhHHhhcCCCceEecCC
Q 039644           57 YIDLNFRRLSRMKV-LIVFDDVTCFS-----QLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEMEA  122 (192)
Q Consensus        57 ~~~~l~~~l~~~~~-LlVlDdv~~~~-----~~~~l~~~~~~~~~~~~iivTtR~~~~~~~~~~~~~~~l~~  122 (192)
                      ..+..++.+.+.+| |+|||.+..--     ..+.+...+.....+..||+|-|+..-.-..-...+.+|..
T Consensus        85 ~~~~a~~~l~~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~p~~l~e~AD~VTEm~~  156 (173)
T TIGR00708        85 AWQHAKEMLADPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGCPQDLLELADLVTEMRP  156 (173)
T ss_pred             HHHHHHHHHhcCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhCceeeeecc
Confidence            34445555555555 99999995221     22333333444455678999999865433332334444443

Alternate name: corrinoid adenosyltransferase.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=94.62  E-value=0.12  Score=46.11  Aligned_cols=79  Identities=14%  Similarity=0.161  Sum_probs=38.8

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-cC--chHHHHhhcCCce-EEEEEeC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV-MP--YIDLNFRRLSRMK-VLIVFDD   76 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~--~~~~l~~~l~~~~-~LlVlDd   76 (192)
                      +|||+||+.+++.+...-...+.+. ++....         ......+.+..+. ..  ....+...++..+ -+|+||+
T Consensus       609 ~GKT~lA~aLa~~l~~~~~~~i~id-~se~~~---------~~~~~~LiG~~pgy~g~~~~g~l~~~v~~~p~~vLllDE  678 (857)
T PRK10865        609 VGKTELCKALANFMFDSDDAMVRID-MSEFME---------KHSVSRLVGAPPGYVGYEEGGYLTEAVRRRPYSVILLDE  678 (857)
T ss_pred             CCHHHHHHHHHHHhhcCCCcEEEEE-hHHhhh---------hhhHHHHhCCCCcccccchhHHHHHHHHhCCCCeEEEee
Confidence            6999999999986533323334443 332111         1112223333222 21  1122333343333 5999999


Q ss_pred             CCCc--hhHHHhhcc
Q 039644           77 VTCF--SQLESLMGS   89 (192)
Q Consensus        77 v~~~--~~~~~l~~~   89 (192)
                      +...  ..+..+...
T Consensus       679 ieka~~~v~~~Ll~i  693 (857)
T PRK10865        679 VEKAHPDVFNILLQV  693 (857)
T ss_pred             hhhCCHHHHHHHHHH
Confidence            9854  334555443

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

Probab=94.54  E-value=0.14  Score=39.03  Aligned_cols=63  Identities=24%  Similarity=0.247  Sum_probs=37.5

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~   79 (192)
                      +|||.||..+.+++...--.+.++           ...+++..+........    ....+.+.+. +-=||||||+-.
T Consensus       116 ~GKThLa~Ai~~~l~~~g~sv~f~-----------~~~el~~~Lk~~~~~~~----~~~~l~~~l~-~~dlLIiDDlG~  178 (254)
T COG1484         116 VGKTHLAIAIGNELLKAGISVLFI-----------TAPDLLSKLKAAFDEGR----LEEKLLRELK-KVDLLIIDDIGY  178 (254)
T ss_pred             CcHHHHHHHHHHHHHHcCCeEEEE-----------EHHHHHHHHHHHHhcCc----hHHHHHHHhh-cCCEEEEecccC
Confidence            699999999999877433344555           35566666655554411    1122222222 223899999964

>cd01131 PilT Pilus retraction ATPase PilT

Probab=94.42  E-value=0.14  Score=37.38  Aligned_cols=100  Identities=9%  Similarity=0.038  Sum_probs=53.3

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-cCchHHHHhhcCCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV-MPYIDLNFRRLSRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~~~~~l~~~l~~~~~LlVlDdv~~   79 (192)
                      +||||++..+...+.......++... .+..   ..... ...+..+... +.+ ....+.++..++..+=++++|.+.+
T Consensus        12 SGKTTll~~ll~~~~~~~~~~i~t~e-~~~E---~~~~~-~~~~i~q~~v-g~~~~~~~~~i~~aLr~~pd~ii~gEird   85 (198)
T cd01131          12 SGKSTTLAAMIDYINKNKTHHILTIE-DPIE---FVHES-KRSLINQREV-GLDTLSFENALKAALRQDPDVILVGEMRD   85 (198)
T ss_pred             CCHHHHHHHHHHHhhhcCCcEEEEEc-CCcc---ccccC-ccceeeeccc-CCCccCHHHHHHHHhcCCcCEEEEcCCCC
Confidence            59999999998877655555555431 1110   00000 0011111000 111 2245566777777788999999987


Q ss_pred             chhHHHhhccCCCCCCCceEEEEecchhHH
Q 039644           80 FSQLESLMGSLDWLTPVSRIILTTRNKQVL  109 (192)
Q Consensus        80 ~~~~~~l~~~~~~~~~~~~iivTtR~~~~~  109 (192)
                      .+.+.......   ..|..++.|+...+..
T Consensus        86 ~e~~~~~l~~a---~~G~~v~~t~Ha~~~~  112 (198)
T cd01131          86 LETIRLALTAA---ETGHLVMSTLHTNSAA  112 (198)
T ss_pred             HHHHHHHHHHH---HcCCEEEEEecCCcHH
Confidence            76655443332   2344577676655443

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.

>PRK10536 hypothetical protein; Provisional

Probab=94.38  E-value=0.2  Score=38.15  Aligned_cols=33  Identities=12%  Similarity=0.331  Sum_probs=23.5

Q ss_pred             eEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEec
Q 039644           69 KVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTR  104 (192)
Q Consensus        69 ~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR  104 (192)
                      .-++|+|.+.+..  +...+..   ..+.+|++|++--
T Consensus       177 ~~~vIvDEaqn~~~~~~k~~lt---R~g~~sk~v~~GD  211 (262)
T PRK10536        177 NAVVILDEAQNVTAAQMKMFLT---RLGENVTVIVNGD  211 (262)
T ss_pred             CCEEEEechhcCCHHHHHHHHh---hcCCCCEEEEeCC
Confidence            4599999998664  4455543   3468899998864

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=94.33  E-value=0.19  Score=36.40  Aligned_cols=66  Identities=18%  Similarity=0.188  Sum_probs=37.6

Q ss_pred             chHHHHhhcCCceE-EEEEeCCCCch-----hHHHhhccCCCCCCCceEEEEecchhHHhhcCCCceEecCC
Q 039644           57 YIDLNFRRLSRMKV-LIVFDDVTCFS-----QLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEMEA  122 (192)
Q Consensus        57 ~~~~l~~~l~~~~~-LlVlDdv~~~~-----~~~~l~~~~~~~~~~~~iivTtR~~~~~~~~~~~~~~~l~~  122 (192)
                      ..+..+..+.+.+| |+|||.+..--     ..+.+...+.....+..||+|-|+..-.-..-...+.+|..
T Consensus       103 ~~~~a~~~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~p~~Lie~ADlVTEm~~  174 (191)
T PRK05986        103 GWEEAKRMLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGAPRELIEAADLVTEMRP  174 (191)
T ss_pred             HHHHHHHHHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCCCHHHHHhCchheeccc
Confidence            34445555655555 99999995322     23344443444456678999999865433322333444443

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=94.19  E-value=0.7  Score=41.41  Aligned_cols=67  Identities=13%  Similarity=0.124  Sum_probs=37.9

Q ss_pred             CceEEEEEeCCCCch-------hHH---HhhccCCCCCCCceEEEEecchhHHhh-------cCCCceEecCCCCHHHHH
Q 039644           67 RMKVLIVFDDVTCFS-------QLE---SLMGSLDWLTPVSRIILTTRNKQVLRN-------WGVSKIYEMEALEYHHAL  129 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~-------~~~---~l~~~~~~~~~~~~iivTtR~~~~~~~-------~~~~~~~~l~~l~~~ea~  129 (192)
                      +.+.+|++|.++...       ..+   -+.+.+.  .+.-++|-+|........       ....+.+.+++++.++..
T Consensus       279 ~~~~ILfIDEih~l~~~g~~~~~~d~~n~Lkp~l~--~G~l~~IgaTT~~e~~~~~~~d~AL~rRf~~i~v~eps~~~~~  356 (852)
T TIGR03345       279 PQPIILFIDEAHTLIGAGGQAGQGDAANLLKPALA--RGELRTIAATTWAEYKKYFEKDPALTRRFQVVKVEEPDEETAI  356 (852)
T ss_pred             CCCeEEEEeChHHhccCCCccccccHHHHhhHHhh--CCCeEEEEecCHHHHhhhhhccHHHHHhCeEEEeCCCCHHHHH
Confidence            467899999996432       111   2333322  122345555543221111       123468999999999999


Q ss_pred             HHHHHh
Q 039644          130 ELFSQH  135 (192)
Q Consensus       130 ~lf~~~  135 (192)
                      +++...
T Consensus       357 ~iL~~~  362 (852)
T TIGR03345       357 RMLRGL  362 (852)
T ss_pred             HHHHHH
Confidence            997543

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.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=94.02  E-value=0.9  Score=34.67  Aligned_cols=68  Identities=13%  Similarity=0.133  Sum_probs=37.4

Q ss_pred             eEEEEEeCCCCc--hhHHHhhccC-------CC---------CCCCceEEEEecchhHHh-------hcCCCceEecCCC
Q 039644           69 KVLIVFDDVTCF--SQLESLMGSL-------DW---------LTPVSRIILTTRNKQVLR-------NWGVSKIYEMEAL  123 (192)
Q Consensus        69 ~~LlVlDdv~~~--~~~~~l~~~~-------~~---------~~~~~~iivTtR~~~~~~-------~~~~~~~~~l~~l  123 (192)
                      ...+++|+++..  +....+...+       ++         ..++.+||.|+.......       ....-..+.+...
T Consensus       106 g~~lllDEi~r~~~~~q~~Ll~~Le~~~~~i~~~~~~~~~i~~~~~frvIaTsN~~~~~g~~~l~~aL~~R~~~i~i~~P  185 (262)
T TIGR02640       106 GFTLVYDEFTRSKPETNNVLLSVFEEGVLELPGKRGTSRYVDVHPEFRVIFTSNPVEYAGVHETQDALLDRLITIFMDYP  185 (262)
T ss_pred             CCEEEEcchhhCCHHHHHHHHHHhcCCeEEccCCCCCCceEecCCCCEEEEeeCCccccceecccHHHHhhcEEEECCCC
Confidence            468999999853  2233332221       21         113668888887432110       0011235667777


Q ss_pred             CHHHHHHHHHHhh
Q 039644          124 EYHHALELFSQHA  136 (192)
Q Consensus       124 ~~~ea~~lf~~~~  136 (192)
                      +.++-.+++..+.
T Consensus       186 ~~~~e~~Il~~~~  198 (262)
T TIGR02640       186 DIDTETAILRAKT  198 (262)
T ss_pred             CHHHHHHHHHHhh
Confidence            7777777777764

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).

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

Probab=93.96  E-value=1.1  Score=35.02  Aligned_cols=61  Identities=13%  Similarity=0.168  Sum_probs=37.6

Q ss_pred             CceEEEEEeCCCCchh--HHHhhccCCCCCCCceEEEEecchhH-Hhhc-CCCceEecCCCCHHH
Q 039644           67 RMKVLIVFDDVTCFSQ--LESLMGSLDWLTPVSRIILTTRNKQV-LRNW-GVSKIYEMEALEYHH  127 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~~--~~~l~~~~~~~~~~~~iivTtR~~~~-~~~~-~~~~~~~l~~l~~~e  127 (192)
                      +..-++++|+++....  -..+...+......+.+|++|....- .... +....+.+.+.+...
T Consensus       108 ~~~kviiidead~mt~~A~nallk~lEep~~~~~~il~~n~~~~il~tI~SRc~~i~f~~~~~~~  172 (325)
T COG0470         108 GGYKVVIIDEADKLTEDAANALLKTLEEPPKNTRFILITNDPSKILPTIRSRCQRIRFKPPSRLE  172 (325)
T ss_pred             CCceEEEeCcHHHHhHHHHHHHHHHhccCCCCeEEEEEcCChhhccchhhhcceeeecCCchHHH
Confidence            4567899999997653  45555555555677888888874332 2212 345567776644333

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=93.89  E-value=0.42  Score=42.06  Aligned_cols=93  Identities=12%  Similarity=0.188  Sum_probs=45.6

Q ss_pred             CCceEEEEEeCCCCch-------------hHHHhhccCCCCC-CCceEEE-EecchhHHhh-c----CCCceEecCCCCH
Q 039644           66 SRMKVLIVFDDVTCFS-------------QLESLMGSLDWLT-PVSRIIL-TTRNKQVLRN-W----GVSKIYEMEALEY  125 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~~-------------~~~~l~~~~~~~~-~~~~iiv-TtR~~~~~~~-~----~~~~~~~l~~l~~  125 (192)
                      ...+.+|+||+++...             ....+...+.... .+..+++ +|........ .    .....+.+...+.
T Consensus       269 ~~~p~il~iDEid~l~~~r~~~~~~~~~~~~~~Ll~~ld~l~~~~~vivI~atn~~~~ld~al~r~gRfd~~i~i~~P~~  348 (733)
T TIGR01243       269 ENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDK  348 (733)
T ss_pred             hcCCcEEEeehhhhhcccccCCcchHHHHHHHHHHHHhhccccCCCEEEEeecCChhhcCHHHhCchhccEEEEeCCcCH
Confidence            4567899999986421             1223333222222 2333444 4443321111 1    1234677777788


Q ss_pred             HHHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCCc
Q 039644          126 HHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIP  161 (192)
Q Consensus       126 ~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  161 (192)
                      ++-.+++...........   ......+++.+.|..
T Consensus       349 ~~R~~Il~~~~~~~~l~~---d~~l~~la~~t~G~~  381 (733)
T TIGR01243       349 RARKEILKVHTRNMPLAE---DVDLDKLAEVTHGFV  381 (733)
T ss_pred             HHHHHHHHHHhcCCCCcc---ccCHHHHHHhCCCCC
Confidence            888888875542211111   112345666666664

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.

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=93.81  E-value=2.5  Score=32.89  Aligned_cols=66  Identities=15%  Similarity=0.228  Sum_probs=42.9

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHH
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFS  133 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~  133 (192)
                      +.+-++|+|+++...  ..+.+...+-+-..++.+|++|.+.. +...+ +....+.+.+ +.++..+.+.
T Consensus       103 ~~~kV~II~~ad~m~~~AaNaLLKtLEEPp~~t~~iL~t~~~~~lLpTI~SRcq~i~f~~-~~~~~~~~L~  172 (290)
T PRK07276        103 GKQQVFIIKDADKMHVNAANSLLKVIEEPQSEIYIFLLTNDENKVLPTIKSRTQIFHFPK-NEAYLIQLLE  172 (290)
T ss_pred             CCcEEEEeehhhhcCHHHHHHHHHHhcCCCCCeEEEEEECChhhCchHHHHcceeeeCCC-cHHHHHHHHH
Confidence            455689999999765  46777777766666777777776644 33333 4456677766 5555555443

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

Probab=93.79  E-value=0.42  Score=42.04  Aligned_cols=22  Identities=0%  Similarity=0.042  Sum_probs=18.2

Q ss_pred             CceEecCCCCHHHHHHHHHHhh
Q 039644          115 SKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus       115 ~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      -+.+.++.++.++..+++....
T Consensus       337 f~~i~v~~p~~~~~~~il~~~~  358 (731)
T TIGR02639       337 FQKIDVGEPSIEETVKILKGLK  358 (731)
T ss_pred             CceEEeCCCCHHHHHHHHHHHH
Confidence            3578999999999999988644

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

Probab=93.62  E-value=0.068  Score=37.99  Aligned_cols=17  Identities=35%  Similarity=0.692  Sum_probs=14.9

Q ss_pred             CchhHHHHHHHHHhhCC
Q 039644            1 IGKTAIARAIFDKISGD   17 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~   17 (192)
                      +|||+|.++++.++..+
T Consensus        35 ~GKT~ll~~~~~~~~~~   51 (185)
T PF13191_consen   35 SGKTSLLRALLDRLAER   51 (185)
T ss_dssp             SSHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhc
Confidence            69999999999987665

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=93.51  E-value=0.97  Score=39.23  Aligned_cols=73  Identities=12%  Similarity=0.179  Sum_probs=40.3

Q ss_pred             CCceEEEEEeCCCCch------------h----HHHhhccCCCCC--CCceEEEEecchhHHhhc-----CCCceEecCC
Q 039644           66 SRMKVLIVFDDVTCFS------------Q----LESLMGSLDWLT--PVSRIILTTRNKQVLRNW-----GVSKIYEMEA  122 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~~------------~----~~~l~~~~~~~~--~~~~iivTtR~~~~~~~~-----~~~~~~~l~~  122 (192)
                      ...+++|+||+++...            .    ...+...+....  .+.-+|.||.........     ...+.+.++.
T Consensus       242 ~~~P~IifIDEiD~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~~~~~vivIaaTN~p~~lD~Al~RpgRfdr~i~v~~  321 (644)
T PRK10733        242 KAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGL  321 (644)
T ss_pred             hcCCcEEEehhHhhhhhccCCCCCCCchHHHHHHHHHHHhhhcccCCCCeeEEEecCChhhcCHHHhCCcccceEEEcCC
Confidence            3468999999996531            1    223322222222  233344466655432221     1245677887


Q ss_pred             CCHHHHHHHHHHhhcC
Q 039644          123 LEYHHALELFSQHAFK  138 (192)
Q Consensus       123 l~~~ea~~lf~~~~~~  138 (192)
                      .+.++-.+++..+...
T Consensus       322 Pd~~~R~~Il~~~~~~  337 (644)
T PRK10733        322 PDVRGREQILKVHMRR  337 (644)
T ss_pred             CCHHHHHHHHHHHhhc
Confidence            7877778887776543

>PRK08118 topology modulation protein; Reviewed

Probab=93.38  E-value=0.28  Score=34.74  Aligned_cols=25  Identities=20%  Similarity=0.392  Sum_probs=19.1

Q ss_pred             CchhHHHHHHHHHhh---CCCcceEEEe
Q 039644            1 IGKTAIARAIFDKIS---GDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~---~~F~~~~wv~   25 (192)
                      +||||||+.+++.+.   -+|+..+|-.
T Consensus        12 sGKSTlak~L~~~l~~~~~~lD~l~~~~   39 (167)
T PRK08118         12 SGKSTLARQLGEKLNIPVHHLDALFWKP   39 (167)
T ss_pred             CCHHHHHHHHHHHhCCCceecchhhccc
Confidence            699999999999743   4467777643

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=93.28  E-value=0.26  Score=35.07  Aligned_cols=114  Identities=9%  Similarity=0.092  Sum_probs=58.7

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC---cCchHHHHhhcCC--ceEEEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV---MPYIDLNFRRLSR--MKVLIVFD   75 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---~~~~~~l~~~l~~--~~~LlVlD   75 (192)
                      +|||++|.+++..   .....+++.....     .+ .++...+.+.....+..   .+....+.+.+.+  ..-.+++|
T Consensus        10 sGKS~~a~~~~~~---~~~~~~y~at~~~-----~d-~em~~rI~~H~~~R~~~w~t~E~~~~l~~~l~~~~~~~~VLID   80 (169)
T cd00544          10 SGKSRFAERLAAE---LGGPVTYIATAEA-----FD-DEMAERIARHRKRRPAHWRTIETPRDLVSALKELDPGDVVLID   80 (169)
T ss_pred             CCHHHHHHHHHHh---cCCCeEEEEccCc-----CC-HHHHHHHHHHHHhCCCCceEeecHHHHHHHHHhcCCCCEEEEE
Confidence            6999999999876   2235566653322     22 23444443322222222   3344445554422  23379999


Q ss_pred             CCCCc-----------------hhHHHhhccCCCCCCCceEEEEecchhHHhhcCCCceEecCCCCHHHHHHHHHHhhc
Q 039644           76 DVTCF-----------------SQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEMEALEYHHALELFSQHAF  137 (192)
Q Consensus        76 dv~~~-----------------~~~~~l~~~~~~~~~~~~iivTtR~~~~~~~~~~~~~~~l~~l~~~ea~~lf~~~~~  137 (192)
                      .+...                 ..+..+...+.  ..+..+|++|.+            +-++..+.+.....|....+
T Consensus        81 clt~~~~n~l~~~~~~~~~~~~~~i~~l~~~l~--~~~~~~viVsnE------------vG~g~vp~~~~~r~f~d~lG  145 (169)
T cd00544          81 CLTLWVTNLLFADLEEWEAAIADEIDALLAAVR--NKPGTLILVSNE------------VGLGVVPENALGRRFRDELG  145 (169)
T ss_pred             cHhHHHHHhCCCccccchhHHHHHHHHHHHHHH--cCCCcEEEEECC------------cCCCCCCCCHHHHHHHHHHH
Confidence            98311                 11222333332  234456766642            44566666667777776653

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.

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=93.24  E-value=0.48  Score=35.26  Aligned_cols=26  Identities=12%  Similarity=0.189  Sum_probs=18.9

Q ss_pred             CchhHHHHHHHHHhhCC------CcceEEEee
Q 039644            1 IGKTAIARAIFDKISGD------FECSCFLEN   26 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~------F~~~~wv~~   26 (192)
                      +|||+||.+++......      -..++|++.
T Consensus        30 sGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~   61 (235)
T cd01123          30 SGKTQLCHQLAVTVQLPIELGGLEGKAVYIDT   61 (235)
T ss_pred             CCHHHHHHHHHHHeeCccccCCCCccEEEEeC
Confidence            69999999998653222      257889873

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 .

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

Probab=93.07  E-value=0.86  Score=34.43  Aligned_cols=46  Identities=15%  Similarity=0.217  Sum_probs=24.9

Q ss_pred             CCceEEEEEeCCC---CchhHHHhhccCC----CCCCCceEEEEecchhHHhh
Q 039644           66 SRMKVLIVFDDVT---CFSQLESLMGSLD----WLTPVSRIILTTRNKQVLRN  111 (192)
Q Consensus        66 ~~~~~LlVlDdv~---~~~~~~~l~~~~~----~~~~~~~iivTtR~~~~~~~  111 (192)
                      +..+|+|.+||+.   .......+...+.    ....+..|..||..++....
T Consensus       104 ~~~kFIlf~DDLsFe~~d~~yk~LKs~LeGgle~~P~NvliyATSNRRHLv~E  156 (249)
T PF05673_consen  104 RPYKFILFCDDLSFEEGDTEYKALKSVLEGGLEARPDNVLIYATSNRRHLVPE  156 (249)
T ss_pred             CCCCEEEEecCCCCCCCcHHHHHHHHHhcCccccCCCcEEEEEecchhhccch
Confidence            3469999999995   2233444433322    22234455556655554444

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=92.65  E-value=0.17  Score=38.58  Aligned_cols=72  Identities=14%  Similarity=0.172  Sum_probs=38.7

Q ss_pred             CchhHHHHHHHHHh--hCCC----cceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-cC---------------ch
Q 039644            1 IGKTAIARAIFDKI--SGDF----ECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV-MP---------------YI   58 (192)
Q Consensus         1 iGKTtLa~~~~~~~--~~~F----~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~---------------~~   58 (192)
                      +|||.|+.+++-.+  ....    ..++|++.-+.     +....+. ++++....+.+. .+               .+
T Consensus        49 sGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~-----f~~~Rl~-~i~~~~~~~~~~~l~~I~v~~~~~~~~l~~~L  122 (256)
T PF08423_consen   49 SGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGT-----FSPERLQ-QIAERFGLDPEEILDNIFVIRVFDLEELLELL  122 (256)
T ss_dssp             SSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSS-----S-HHHHH-HHHHHTTS-HHHHHHTEEEEE-SSHHHHHHHH
T ss_pred             cccchHHHHHHHHhhcccccccCCCceEEEeCCCC-----CCHHHHH-HHhhccccccchhhhceeeeecCCHHHHHHHH
Confidence            69999999998743  2222    24788874333     5555554 455543221111 11               23


Q ss_pred             HHHHhhc-CCceEEEEEeCCC
Q 039644           59 DLNFRRL-SRMKVLIVFDDVT   78 (192)
Q Consensus        59 ~~l~~~l-~~~~~LlVlDdv~   78 (192)
                      ..+...+ .++--|||+|.+.
T Consensus       123 ~~l~~~l~~~~ikLIVIDSIa  143 (256)
T PF08423_consen  123 EQLPKLLSESKIKLIVIDSIA  143 (256)
T ss_dssp             HHHHHHHHHSCEEEEEEETSS
T ss_pred             HHHHhhccccceEEEEecchH
Confidence            3333333 2345599999995

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 ....

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

Probab=92.65  E-value=0.34  Score=38.88  Aligned_cols=124  Identities=19%  Similarity=0.282  Sum_probs=70.3

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHh-cCCCC--cC--------chHHHHh--hc--
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNIL-KDKNV--MP--------YIDLNFR--RL--   65 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~--~~--------~~~~l~~--~l--   65 (192)
                      .|||.+.+++.+....   ..+|+..+..     ++...+...|+.+.. ...+.  .+        .+..+.+  ..  
T Consensus        41 TGKT~~~r~~l~~~n~---~~vw~n~~ec-----ft~~~lle~IL~~~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~  112 (438)
T KOG2543|consen   41 TGKTYLVRQLLRKLNL---ENVWLNCVEC-----FTYAILLEKILNKSQLADKDGDKVEGDAENFSDFIYLLVQWPAATN  112 (438)
T ss_pred             CchhHHHHHHHhhcCC---cceeeehHHh-----ccHHHHHHHHHHHhccCCCchhhhhhHHHHHHHHHHHHHhhHHhhc
Confidence            5999999999997732   3489886555     788899999999984 22222  22        1222222  11  


Q ss_pred             CCceEEEEEeCCCCchhHHHh-----h---ccCCCCCCCceEEEEecchhH-Hhh--cCCC--ceEecCCCCHHHHHHHH
Q 039644           66 SRMKVLIVFDDVTCFSQLESL-----M---GSLDWLTPVSRIILTTRNKQV-LRN--WGVS--KIYEMEALEYHHALELF  132 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~~~~~~l-----~---~~~~~~~~~~~iivTtR~~~~-~~~--~~~~--~~~~l~~l~~~ea~~lf  132 (192)
                      +++..+|||||++...+.+..     .   ..++  .+ .-+|+++-.... ...  .|+.  -++..+.-+.+|...++
T Consensus       113 ~d~~~~liLDnad~lrD~~a~ll~~l~~L~el~~--~~-~i~iils~~~~e~~y~~n~g~~~i~~l~fP~Ys~~e~~~Il  189 (438)
T KOG2543|consen  113 RDQKVFLILDNADALRDMDAILLQCLFRLYELLN--EP-TIVIILSAPSCEKQYLINTGTLEIVVLHFPQYSVEETQVIL  189 (438)
T ss_pred             cCceEEEEEcCHHhhhccchHHHHHHHHHHHHhC--CC-ceEEEEeccccHHHhhcccCCCCceEEecCCCCHHHHHHHH
Confidence            145899999999876553321     1   1121  12 223444322111 111  1222  24556677777777777


Q ss_pred             HHh
Q 039644          133 SQH  135 (192)
Q Consensus       133 ~~~  135 (192)
                      .+.
T Consensus       190 ~~~  192 (438)
T KOG2543|consen  190 SRD  192 (438)
T ss_pred             hcC
Confidence            654

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

Probab=92.46  E-value=0.26  Score=40.57  Aligned_cols=72  Identities=11%  Similarity=0.125  Sum_probs=39.1

Q ss_pred             CchhHHHHHHHHHhh--CCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC---cC--chHHHHhhc--CCceEE
Q 039644            1 IGKTAIARAIFDKIS--GDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV---MP--YIDLNFRRL--SRMKVL   71 (192)
Q Consensus         1 iGKTtLa~~~~~~~~--~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---~~--~~~~l~~~l--~~~~~L   71 (192)
                      +|||++|+.++..+.  ..|..+.|+. .++.    ....+++.    ...+....   ..  ..+.+....  .+++++
T Consensus       205 tGKT~lA~~la~~l~~~~~~~~v~~Vt-FHps----ySYeDFI~----G~rP~~vgy~~~~G~f~~~~~~A~~~p~~~~v  275 (459)
T PRK11331        205 VGKTFVARRLAYLLTGEKAPQRVNMVQ-FHQS----YSYEDFIQ----GYRPNGVGFRRKDGIFYNFCQQAKEQPEKKYV  275 (459)
T ss_pred             CCHHHHHHHHHHHhcCCcccceeeEEe-eccc----ccHHHHhc----ccCCCCCCeEecCchHHHHHHHHHhcccCCcE
Confidence            699999999999764  3456666776 2221    33333332    11111111   11  122222222  246899


Q ss_pred             EEEeCCCCch
Q 039644           72 IVFDDVTCFS   81 (192)
Q Consensus        72 lVlDdv~~~~   81 (192)
                      +|+|.++...
T Consensus       276 liIDEINRan  285 (459)
T PRK11331        276 FIIDEINRAN  285 (459)
T ss_pred             EEEehhhccC
Confidence            9999998543

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

Probab=92.46  E-value=2.9  Score=31.66  Aligned_cols=38  Identities=24%  Similarity=0.171  Sum_probs=25.5

Q ss_pred             HHHHHHhC-CCchHHHHHHHHhccCCHHHHHHHHHHHHh
Q 039644          151 SNVTKYAQ-GIPLALKVLSCFLHKREKEVWESAIDKLQR  188 (192)
Q Consensus       151 ~~i~~~~~-g~Plai~~~~~~l~~~~~~~w~~~l~~l~~  188 (192)
                      +.+++.|+ .||+.++-+-........++-.++++++.+
T Consensus       228 enVfKv~d~PhP~~v~~ml~~~~~~~~~~A~~il~~lw~  266 (333)
T KOG0991|consen  228 ENVFKVCDEPHPLLVKKMLQACLKRNIDEALKILAELWK  266 (333)
T ss_pred             hhhhhccCCCChHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            34566665 788888877776655556666667766654

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=92.27  E-value=0.53  Score=34.87  Aligned_cols=26  Identities=15%  Similarity=0.190  Sum_probs=21.1

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEee
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLEN   26 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~   26 (192)
                      +|||++|.+++......-..++|++.
T Consensus        34 sGKT~l~~~la~~~~~~~~~v~yi~~   59 (225)
T PRK09361         34 SGKTNICLQLAVEAAKNGKKVIYIDT   59 (225)
T ss_pred             CCHHHHHHHHHHHHHHCCCeEEEEEC
Confidence            59999999999976555567889873

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

Probab=92.25  E-value=2.8  Score=36.09  Aligned_cols=139  Identities=17%  Similarity=0.313  Sum_probs=75.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhc-CCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRL-SRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l-~~~~~LlVlDdv~~   79 (192)
                      +|||-||+.|+++-..+|     +++=++             +++...-+.++  ..++.+.... ..-+|+|.||.++.
T Consensus       556 CGKTLlAKAVANEag~NF-----isVKGP-------------ELlNkYVGESE--rAVR~vFqRAR~saPCVIFFDEiDa  615 (802)
T KOG0733|consen  556 CGKTLLAKAVANEAGANF-----ISVKGP-------------ELLNKYVGESE--RAVRQVFQRARASAPCVIFFDEIDA  615 (802)
T ss_pred             ccHHHHHHHHhhhccCce-----EeecCH-------------HHHHHHhhhHH--HHHHHHHHHhhcCCCeEEEecchhh
Confidence            799999999999887665     331111             22222222211  0333333333 46799999999974


Q ss_pred             ch-------------hHHHhhccCCCCC--CCceEEEEecchhHHhhc-----CCCceEecCCCCHHHHHHHHHHhhcCC
Q 039644           80 FS-------------QLESLMGSLDWLT--PVSRIILTTRNKQVLRNW-----GVSKIYEMEALEYHHALELFSQHAFKR  139 (192)
Q Consensus        80 ~~-------------~~~~l~~~~~~~~--~~~~iivTtR~~~~~~~~-----~~~~~~~l~~l~~~ea~~lf~~~~~~~  139 (192)
                      ..             ...++..-+....  .|.-||-.|..+++....     .-.+.+-++.-+.+|-.++++...-..
T Consensus       616 L~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDpAiLRPGRlDk~LyV~lPn~~eR~~ILK~~tkn~  695 (802)
T KOG0733|consen  616 LVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDPAILRPGRLDKLLYVGLPNAEERVAILKTITKNT  695 (802)
T ss_pred             cCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcccchhhcCCCccCceeeecCCCHHHHHHHHHHHhccC
Confidence            21             1345544444332  344455555555443332     224567777778888888887766321


Q ss_pred             C---CCCccHHHHHHHHHHHhCCCc
Q 039644          140 N---HPDVGYEKLSSNVTKYAQGIP  161 (192)
Q Consensus       140 ~---~~~~~~~~~~~~i~~~~~g~P  161 (192)
                      .   .++-.+++++..  .+|.|+-
T Consensus       696 k~pl~~dVdl~eia~~--~~c~gft  718 (802)
T KOG0733|consen  696 KPPLSSDVDLDEIARN--TKCEGFT  718 (802)
T ss_pred             CCCCCcccCHHHHhhc--ccccCCc
Confidence            1   123345544442  3455553

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=92.20  E-value=0.64  Score=33.97  Aligned_cols=26  Identities=15%  Similarity=0.183  Sum_probs=21.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEee
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLEN   26 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~   26 (192)
                      +|||+++.+++......-..++|++.
T Consensus        23 sGKT~l~~~~~~~~~~~g~~v~yi~~   48 (209)
T TIGR02237        23 SGKTNICMILAVNAARQGKKVVYIDT   48 (209)
T ss_pred             CCHHHHHHHHHHHHHhCCCeEEEEEC
Confidence            69999999999876555677899983

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

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=92.13  E-value=0.81  Score=37.17  Aligned_cols=69  Identities=14%  Similarity=0.180  Sum_probs=43.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC----cC-chHHHHhhcC-CceEEEEE
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV----MP-YIDLNFRRLS-RMKVLIVF   74 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~----~~-~~~~l~~~l~-~~~~LlVl   74 (192)
                      ||||||..+++.++..+. .+.+|+.  +     .....+- --.+.+.-..+.    .+ -.+.+...+. .++-++|+
T Consensus       104 IGKSTLLLQva~~lA~~~-~vLYVsG--E-----ES~~Qik-lRA~RL~~~~~~l~l~aEt~~e~I~~~l~~~~p~lvVI  174 (456)
T COG1066         104 IGKSTLLLQVAARLAKRG-KVLYVSG--E-----ESLQQIK-LRADRLGLPTNNLYLLAETNLEDIIAELEQEKPDLVVI  174 (456)
T ss_pred             CCHHHHHHHHHHHHHhcC-cEEEEeC--C-----cCHHHHH-HHHHHhCCCccceEEehhcCHHHHHHHHHhcCCCEEEE
Confidence            799999999999988776 7888862  1     1222221 223334322222    11 4555666664 56889999


Q ss_pred             eCCC
Q 039644           75 DDVT   78 (192)
Q Consensus        75 Ddv~   78 (192)
                      |.+.
T Consensus       175 DSIQ  178 (456)
T COG1066         175 DSIQ  178 (456)
T ss_pred             eccc
Confidence            9995

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

Probab=92.03  E-value=5.5  Score=33.14  Aligned_cols=131  Identities=20%  Similarity=0.262  Sum_probs=74.9

Q ss_pred             CchhHHHHHHHHHhhCCCcc--eEEEeeccccccCCCChHHHHHHHHHHHh----cCCCCcCchHHHHhhcCC--ceEEE
Q 039644            1 IGKTAIARAIFDKISGDFEC--SCFLENVREESQRPGGLACLRQKLLSNIL----KDKNVMPYIDLNFRRLSR--MKVLI   72 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~--~~wv~~~~~~~~~~~~~~~~~~~l~~~~~----~~~~~~~~~~~l~~~l~~--~~~Ll   72 (192)
                      .|||.+...++.+.......  ++++...+-     ....+++..+...+.    +.+.+.+....+..++.+  ..+|+
T Consensus       186 tgkt~~l~rvl~~~~~~~~~~~~v~inc~sl-----~~~~aiF~kI~~~~~q~~~s~~~~~~~~~~~~~h~~q~k~~~ll  260 (529)
T KOG2227|consen  186 TGKTALLSRVLDSLSKSSKSPVTVYINCTSL-----TEASAIFKKIFSSLLQDLVSPGTGMQHLEKFEKHTKQSKFMLLL  260 (529)
T ss_pred             cchHHHHHHHHHhhhhhcccceeEEEeeccc-----cchHHHHHHHHHHHHHHhcCCchhHHHHHHHHHHHhcccceEEE
Confidence            49999999999876554433  355553321     356677777776662    222213356666666654  36899


Q ss_pred             EEeCCCCchh-----HHHhhccCCCCCCCceEEEEe---------cchhHHhh-c-CCCceEecCCCCHHHHHHHHHHhh
Q 039644           73 VFDDVTCFSQ-----LESLMGSLDWLTPVSRIILTT---------RNKQVLRN-W-GVSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus        73 VlDdv~~~~~-----~~~l~~~~~~~~~~~~iivTt---------R~~~~~~~-~-~~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      |+|..+....     +..++ .++. -+++++|+.-         |.-.-... . -....+..++-+.++..++|..+.
T Consensus       261 VlDEmD~L~tr~~~vLy~lF-ewp~-lp~sr~iLiGiANslDlTdR~LprL~~~~~~~P~~l~F~PYTk~qI~~Il~~rl  338 (529)
T KOG2227|consen  261 VLDEMDHLITRSQTVLYTLF-EWPK-LPNSRIILIGIANSLDLTDRFLPRLNLDLTIKPKLLVFPPYTKDQIVEILQQRL  338 (529)
T ss_pred             EechhhHHhhcccceeeeeh-hccc-CCcceeeeeeehhhhhHHHHHhhhhhhccCCCCceeeecCCCHHHHHHHHHHHH
Confidence            9999974321     11111 1222 2345554432         21111111 0 135678889999999999998876


Q ss_pred             cC
Q 039644          137 FK  138 (192)
Q Consensus       137 ~~  138 (192)
                      ..
T Consensus       339 ~~  340 (529)
T KOG2227|consen  339 SE  340 (529)
T ss_pred             hc
Confidence            43

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

Probab=92.00  E-value=0.97  Score=33.37  Aligned_cols=26  Identities=12%  Similarity=0.074  Sum_probs=19.8

Q ss_pred             CchhHHHHHHHHHhhCCC------cceEEEee
Q 039644            1 IGKTAIARAIFDKISGDF------ECSCFLEN   26 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F------~~~~wv~~   26 (192)
                      +|||+||.+++.......      ..++|++.
T Consensus        30 sGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~   61 (226)
T cd01393          30 SGKTQLCLQLAVEAQLPGELGGLEGKVVYIDT   61 (226)
T ss_pred             CChhHHHHHHHHHhhcccccCCCcceEEEEec
Confidence            699999999988754444      56788873

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.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=91.99  E-value=3.4  Score=37.21  Aligned_cols=67  Identities=7%  Similarity=-0.014  Sum_probs=36.2

Q ss_pred             CceEEEEEeCCCCch---------h-HHHhhccCCCCCCCceEEEEecchhHHh-------hcCCCceEecCCCCHHHHH
Q 039644           67 RMKVLIVFDDVTCFS---------Q-LESLMGSLDWLTPVSRIILTTRNKQVLR-------NWGVSKIYEMEALEYHHAL  129 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~---------~-~~~l~~~~~~~~~~~~iivTtR~~~~~~-------~~~~~~~~~l~~l~~~ea~  129 (192)
                      +.+.+|++|+++...         + .+.+.+.+ .. ..-++|-+|.......       ....-..+.++..+.++..
T Consensus       265 ~~~~ILfIDEih~l~~~g~~~~~~d~~~~Lk~~l-~~-g~i~~IgaTt~~e~r~~~~~d~al~rRf~~i~v~~p~~~~~~  342 (852)
T TIGR03346       265 EGQIILFIDELHTLVGAGKAEGAMDAGNMLKPAL-AR-GELHCIGATTLDEYRKYIEKDAALERRFQPVFVDEPTVEDTI  342 (852)
T ss_pred             CCCeEEEeccHHHhhcCCCCcchhHHHHHhchhh-hc-CceEEEEeCcHHHHHHHhhcCHHHHhcCCEEEeCCCCHHHHH
Confidence            468999999997432         1 12222222 11 2234444443332211       1123356788888999988


Q ss_pred             HHHHHh
Q 039644          130 ELFSQH  135 (192)
Q Consensus       130 ~lf~~~  135 (192)
                      .++...
T Consensus       343 ~iL~~~  348 (852)
T TIGR03346       343 SILRGL  348 (852)
T ss_pred             HHHHHH
Confidence            887654

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.

>PRK04296 thymidine kinase; Provisional

Probab=91.98  E-value=0.2  Score=36.24  Aligned_cols=97  Identities=12%  Similarity=-0.025  Sum_probs=46.9

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCC-----C-cCchHHHHhhcCCceEEEEE
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKN-----V-MPYIDLNFRRLSRMKVLIVF   74 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-----~-~~~~~~l~~~l~~~~~LlVl   74 (192)
                      .||||+|..++.+...+...++.+. ..      ++.......+...++..-.     . .+....+.. ..++.-++|+
T Consensus        13 sGKTT~~l~~~~~~~~~g~~v~i~k-~~------~d~~~~~~~i~~~lg~~~~~~~~~~~~~~~~~~~~-~~~~~dvviI   84 (190)
T PRK04296         13 SGKSTELLQRAYNYEERGMKVLVFK-PA------IDDRYGEGKVVSRIGLSREAIPVSSDTDIFELIEE-EGEKIDCVLI   84 (190)
T ss_pred             CHHHHHHHHHHHHHHHcCCeEEEEe-cc------ccccccCCcEecCCCCcccceEeCChHHHHHHHHh-hCCCCCEEEE
Confidence            5999999999998755544444342 10      0000001112222221100     0 112222322 2224458999


Q ss_pred             eCCCCc--hhHHHhhccCCCCCCCceEEEEecchh
Q 039644           75 DDVTCF--SQLESLMGSLDWLTPVSRIILTTRNKQ  107 (192)
Q Consensus        75 Ddv~~~--~~~~~l~~~~~~~~~~~~iivTtR~~~  107 (192)
                      |.+.-.  ++...+...+.  ..|..|++|.+...
T Consensus        85 DEaq~l~~~~v~~l~~~l~--~~g~~vi~tgl~~~  117 (190)
T PRK04296         85 DEAQFLDKEQVVQLAEVLD--DLGIPVICYGLDTD  117 (190)
T ss_pred             EccccCCHHHHHHHHHHHH--HcCCeEEEEecCcc
Confidence            999643  22333333221  35678999988743

>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=91.91  E-value=0.51  Score=37.87  Aligned_cols=94  Identities=15%  Similarity=0.152  Sum_probs=53.7

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCC--
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVT--   78 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~--   78 (192)
                      .|||.|+-.+|+.+...=...             .....++..+-+.+.......+.+..+...+.++..||+||.+.  
T Consensus        73 ~GKT~Lmd~f~~~lp~~~k~R-------------~HFh~Fm~~vh~~l~~~~~~~~~l~~va~~l~~~~~lLcfDEF~V~  139 (362)
T PF03969_consen   73 RGKTMLMDLFYDSLPIKRKRR-------------VHFHEFMLDVHSRLHQLRGQDDPLPQVADELAKESRLLCFDEFQVT  139 (362)
T ss_pred             CchhHHHHHHHHhCCcccccc-------------ccccHHHHHHHHHHHHHhCCCccHHHHHHHHHhcCCEEEEeeeecc
Confidence            599999999999653311111             23334455554444433322335666777778888899999986  


Q ss_pred             Cchh---HHHhhccCCCCCCCceEEEEecchhHHh
Q 039644           79 CFSQ---LESLMGSLDWLTPVSRIILTTRNKQVLR  110 (192)
Q Consensus        79 ~~~~---~~~l~~~~~~~~~~~~iivTtR~~~~~~  110 (192)
                      +..+   +..+...+-  ..|. +||+|.|.....
T Consensus       140 DiaDAmil~rLf~~l~--~~gv-vlVaTSN~~P~~  171 (362)
T PF03969_consen  140 DIADAMILKRLFEALF--KRGV-VLVATSNRPPED  171 (362)
T ss_pred             chhHHHHHHHHHHHHH--HCCC-EEEecCCCChHH
Confidence            2222   444544432  3455 666665544433

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

>TIGR00763 lon ATP-dependent protease La

Probab=91.75  E-value=0.93  Score=40.23  Aligned_cols=24  Identities=13%  Similarity=0.159  Sum_probs=18.2

Q ss_pred             CCCceEecCCCCHHHHHHHHHHhh
Q 039644          113 GVSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus       113 ~~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      .....+++.+++.++-.+++..+.
T Consensus       482 ~R~~vi~~~~~~~~e~~~I~~~~l  505 (775)
T TIGR00763       482 DRMEVIELSGYTEEEKLEIAKKYL  505 (775)
T ss_pred             CCeeEEecCCCCHHHHHHHHHHHH
Confidence            344688999999988888876543

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.

>COG5635 Predicted NTPase (NACHT family) [Signal transduction mechanisms]

Probab=91.75  E-value=1.8  Score=38.79  Aligned_cols=181  Identities=15%  Similarity=0.166  Sum_probs=88.3

Q ss_pred             CchhHHHHHHHHHhhCCC----cceEEEeecc-ccccCCCChH-HHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEE
Q 039644            1 IGKTAIARAIFDKISGDF----ECSCFLENVR-EESQRPGGLA-CLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVF   74 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F----~~~~wv~~~~-~~~~~~~~~~-~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVl   74 (192)
                      .||||+...++-...++.    +..+++..-. ..... +... .+...+...+.....-..........++..++|+.+
T Consensus       233 sGKTtfl~~lA~~~~~~~~~~~~vpi~~~l~~~~~~~~-~~~q~~~~~~l~~~~~~~~~~~~~~~~~~e~l~~g~~llLl  311 (824)
T COG5635         233 SGKTTFLQRLALWLAQRTLEPEDVPIFLLLNAFALARK-FEKQLSLIDYLAEELFSQGIAKQLIEAHQELLKTGKLLLLL  311 (824)
T ss_pred             CCceehHHHHHHHhccCcCCcccCceeeechhHHHhhh-hHhhccHHHHHHHHHhccCCcchhhHHHHHHHhccchhhHh
Confidence            599999999988543222    2334443110 00000 1111 222222222222221122334345788999999999


Q ss_pred             eCCCCchh---------HHHhhccCCCCCCCceEEEEecchhHHhhcCCCceEecCCCCHHHHHHHHH--------Hhhc
Q 039644           75 DDVTCFSQ---------LESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEMEALEYHHALELFS--------QHAF  137 (192)
Q Consensus        75 Ddv~~~~~---------~~~l~~~~~~~~~~~~iivTtR~~~~~~~~~~~~~~~l~~l~~~ea~~lf~--------~~~~  137 (192)
                      |.++....         +..+.+.+    +.+++|+|+|..........-..+++..+.+........        ...+
T Consensus       312 DGlDe~~~~~~~~~~~~i~~f~~~~----~~~~~iltcR~~~~~~~~~~f~~~ei~~~~~~~i~~~~~~~~~~~~~~~~~  387 (824)
T COG5635         312 DGLDELEPKNQRALIREINKFLQEY----PDAQVLLTCRPDTYKEEFKGFAVFEIYKFLDLQINQFILYQWLDAFIEDWF  387 (824)
T ss_pred             hccchhhhhhHHHHHHHHHHHhhhc----cCCeEEEEeccchhhhhhhhhhhccchhhhHHHHHHHHHHHHHHHHHHhhh
Confidence            99986532         33333333    467899999875544443223334444444443332221        1111


Q ss_pred             CCCCCC-----ccHHHHHHHHHHHhCCCchHHHHHHHHhcc------CCHHHHHHHHHHH
Q 039644          138 KRNHPD-----VGYEKLSSNVTKYAQGIPLALKVLSCFLHK------REKEVWESAIDKL  186 (192)
Q Consensus       138 ~~~~~~-----~~~~~~~~~i~~~~~g~Plai~~~~~~l~~------~~~~~w~~~l~~l  186 (192)
                      ......     ..+......-++.....|+.+.+.+..-..      ...+-++.+++.+
T Consensus       388 ~~~~~~~~~~~~~l~~~~~~~ik~l~~~p~~L~l~c~~~~~~~~lP~~~~~ly~~~~~~~  447 (824)
T COG5635         388 GDSRLLAKKLLERLKLPENRRIKELALTPLLLALECLIWQAQGDLPESRAELYEQAVDAL  447 (824)
T ss_pred             cccchhhHHHHHHhcchhhHHHHHhccCHHHHHHHHHhhhHHhhCCCCcHHHHHHHHHHH
Confidence            111101     111122334455567889999998854442      1155566655544

>PRK12678 transcription termination factor Rho; Provisional

Probab=91.50  E-value=0.4  Score=40.79  Aligned_cols=77  Identities=21%  Similarity=0.317  Sum_probs=42.8

Q ss_pred             CchhHHHHHHHHHhhCCC-cceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC--cC-------chHHHHhhc--CCc
Q 039644            1 IGKTAIARAIFDKISGDF-ECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV--MP-------YIDLNFRRL--SRM   68 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F-~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--~~-------~~~~l~~~l--~~~   68 (192)
                      +|||+|+..+++.+.... ++.+++..+.+-   +..+.++...+--.+.....+  ..       ..-.+.+++  .++
T Consensus       427 aGKTtLL~~IAn~i~~n~~~~~~ivvLIgER---peEVtdm~rsVkgeVVasT~D~p~~~~~~~a~~ai~~Ae~fre~G~  503 (672)
T PRK12678        427 AGKTTILQNIANAITTNNPECHLMVVLVDER---PEEVTDMQRSVKGEVIASTFDRPPSDHTTVAELAIERAKRLVELGK  503 (672)
T ss_pred             CCHHHHHHHHHHHHhhcCCCeEEEEEEEeCc---hhhHHHHHHhccceEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence            599999999999775443 444455545442   234555544431111111111  11       222344444  578


Q ss_pred             eEEEEEeCCCCc
Q 039644           69 KVLIVFDDVTCF   80 (192)
Q Consensus        69 ~~LlVlDdv~~~   80 (192)
                      .+||++|++...
T Consensus       504 dVlillDSlTR~  515 (672)
T PRK12678        504 DVVVLLDSITRL  515 (672)
T ss_pred             CEEEEEeCchHH
Confidence            999999999644

>PHA00729 NTP-binding motif containing protein

Probab=91.37  E-value=1.1  Score=33.46  Aligned_cols=15  Identities=27%  Similarity=0.257  Sum_probs=13.1

Q ss_pred             CchhHHHHHHHHHhh
Q 039644            1 IGKTAIARAIFDKIS   15 (192)
Q Consensus         1 iGKTtLa~~~~~~~~   15 (192)
                      +||||||..+++++-
T Consensus        28 vGKT~LA~aLa~~l~   42 (226)
T PHA00729         28 SGKTTYALKVARDVF   42 (226)
T ss_pred             CCHHHHHHHHHHHHH
Confidence            699999999999753

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

Probab=91.34  E-value=0.61  Score=41.17  Aligned_cols=75  Identities=12%  Similarity=0.168  Sum_probs=38.0

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-cC--chHHHHhhcCCc-eEEEEEeC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV-MP--YIDLNFRRLSRM-KVLIVFDD   76 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~--~~~~l~~~l~~~-~~LlVlDd   76 (192)
                      +|||++|+.++..+...   .+.++ ++..... ...        ..+.+..+. ..  ....+...++.+ ..+++||+
T Consensus       499 vGKT~lAk~LA~~l~~~---~i~id-~se~~~~-~~~--------~~LiG~~~gyvg~~~~g~L~~~v~~~p~sVlllDE  565 (758)
T PRK11034        499 VGKTEVTVQLSKALGIE---LLRFD-MSEYMER-HTV--------SRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDE  565 (758)
T ss_pred             CCHHHHHHHHHHHhCCC---cEEee-chhhccc-ccH--------HHHcCCCCCcccccccchHHHHHHhCCCcEEEecc
Confidence            69999999999977432   23333 3332211 111        222222222 11  112233344433 46999999


Q ss_pred             CCCch--hHHHhhc
Q 039644           77 VTCFS--QLESLMG   88 (192)
Q Consensus        77 v~~~~--~~~~l~~   88 (192)
                      ++..+  .++.+..
T Consensus       566 ieka~~~v~~~LLq  579 (758)
T PRK11034        566 IEKAHPDVFNLLLQ  579 (758)
T ss_pred             HhhhhHHHHHHHHH
Confidence            98654  2444443

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=91.24  E-value=1.6  Score=33.63  Aligned_cols=98  Identities=17%  Similarity=0.180  Sum_probs=54.0

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHh--cCCC-----C-cC---chHHHHhhcC-Cc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNIL--KDKN-----V-MP---YIDLNFRRLS-RM   68 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~--~~~~-----~-~~---~~~~l~~~l~-~~   68 (192)
                      +|||||.+.++..+... .+.+++. .....     ..+-..++.....  .+..     + .+   -..-+...+. ..
T Consensus       122 ~GKttl~~~l~~~~~~~-~G~i~~~-g~~v~-----~~d~~~ei~~~~~~~~q~~~~~r~~v~~~~~k~~~~~~~i~~~~  194 (270)
T TIGR02858       122 CGKTTLLRDLARILSTG-ISQLGLR-GKKVG-----IVDERSEIAGCVNGVPQHDVGIRTDVLDGCPKAEGMMMLIRSMS  194 (270)
T ss_pred             CCHHHHHHHHhCccCCC-CceEEEC-CEEee-----cchhHHHHHHHhcccccccccccccccccchHHHHHHHHHHhCC
Confidence            59999999999876533 4556664 22211     1111122222211  1111     1 11   1222333333 47


Q ss_pred             eEEEEEeCCCCchhHHHhhccCCCCCCCceEEEEecchhH
Q 039644           69 KVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQV  108 (192)
Q Consensus        69 ~~LlVlDdv~~~~~~~~l~~~~~~~~~~~~iivTtR~~~~  108 (192)
                      +-++++|.+.....+..+...+.   .|..+|+||....+
T Consensus       195 P~villDE~~~~e~~~~l~~~~~---~G~~vI~ttH~~~~  231 (270)
T TIGR02858       195 PDVIVVDEIGREEDVEALLEALH---AGVSIIATAHGRDV  231 (270)
T ss_pred             CCEEEEeCCCcHHHHHHHHHHHh---CCCEEEEEechhHH
Confidence            88999999987776766655542   46779999986554

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.

>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=91.12  E-value=0.9  Score=33.68  Aligned_cols=73  Identities=16%  Similarity=0.240  Sum_probs=41.4

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHh-------cC-CCC--cC----------chHH
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNIL-------KD-KNV--MP----------YIDL   60 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~-------~~-~~~--~~----------~~~~   60 (192)
                      +|||+|+.++++.....  .++++. +++   .+..+.++...+...-.       .. .++  ..          ..++
T Consensus        26 ~GKt~Ll~~i~~~~~~d--~~V~~~-iGe---r~~Ev~~~~~~~~~~~~~~~t~vv~~t~~~~~~~r~~~~~~a~t~AEy   99 (215)
T PF00006_consen   26 VGKTVLLQEIANNQDAD--VVVYAL-IGE---RGREVTEFIEELKGEGALERTVVVAATSDEPPAARYRAPYTALTIAEY   99 (215)
T ss_dssp             SSHHHHHHHHHHHCTTT--EEEEEE-ESE---CHHHHHHHHHHHHHTTGGGGEEEEEEETTS-HHHHHHHHHHHHHHHHH
T ss_pred             cccchhhHHHHhccccc--ceeeee-ccc---cchhHHHHHHHHhhcccccccccccccchhhHHHHhhhhccchhhhHH
Confidence            59999999999987533  335554 222   11345566655543311       01 111  11          2333


Q ss_pred             HHhhcCCceEEEEEeCCCCch
Q 039644           61 NFRRLSRMKVLIVFDDVTCFS   81 (192)
Q Consensus        61 l~~~l~~~~~LlVlDdv~~~~   81 (192)
                      ++.  .+++.|+++||+....
T Consensus       100 frd--~G~dVlli~Dsltr~a  118 (215)
T PF00006_consen  100 FRD--QGKDVLLIIDSLTRWA  118 (215)
T ss_dssp             HHH--TTSEEEEEEETHHHHH
T ss_pred             Hhh--cCCceeehhhhhHHHH
Confidence            333  7899999999996543

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 ....

>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=91.10  E-value=0.26  Score=36.18  Aligned_cols=101  Identities=16%  Similarity=0.197  Sum_probs=46.6

Q ss_pred             CchhHHHHHHHHH--hhCCCcceEEEeecccc--ccC--CCC----hHHHHHHHHHHHhcCCCCcCchHHH---------
Q 039644            1 IGKTAIARAIFDK--ISGDFECSCFLENVREE--SQR--PGG----LACLRQKLLSNILKDKNVMPYIDLN---------   61 (192)
Q Consensus         1 iGKTtLa~~~~~~--~~~~F~~~~wv~~~~~~--~~~--~~~----~~~~~~~l~~~~~~~~~~~~~~~~l---------   61 (192)
                      .|||.||...+-+  ....|+.++++.-.-+.  ...  |-+    ....+..+.+-+..--.. +..+.+         
T Consensus        30 TGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~~~~lGflpG~~~eK~~p~~~p~~d~l~~~~~~-~~~~~~~~~~~Ie~~  108 (205)
T PF02562_consen   30 TGKTFLALAAALELVKEGEYDKIIITRPPVEAGEDLGFLPGDLEEKMEPYLRPIYDALEELFGK-EKLEELIQNGKIEIE  108 (205)
T ss_dssp             SSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TTTHHHHHHHTTTS-T-TCHHHHHHTTSEEEE
T ss_pred             CcHHHHHHHHHHHHHHhCCCcEEEEEecCCCCccccccCCCCHHHHHHHHHHHHHHHHHHHhCh-HhHHHHhhcCeEEEE
Confidence            5999999999874  35778888777522211  000  111    111122222222211000 011111         


Q ss_pred             -HhhcCC---ceEEEEEeCCCCc--hhHHHhhccCCCCCCCceEEEEecc
Q 039644           62 -FRRLSR---MKVLIVFDDVTCF--SQLESLMGSLDWLTPVSRIILTTRN  105 (192)
Q Consensus        62 -~~~l~~---~~~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~iivTtR~  105 (192)
                       ..++++   .+..+|+|.+.+.  +++..+...   .+.+||+|++--.
T Consensus       109 ~~~~iRGrt~~~~~iIvDEaQN~t~~~~k~ilTR---~g~~skii~~GD~  155 (205)
T PF02562_consen  109 PLAFIRGRTFDNAFIIVDEAQNLTPEELKMILTR---IGEGSKIIITGDP  155 (205)
T ss_dssp             EGGGGTT--B-SEEEEE-SGGG--HHHHHHHHTT---B-TT-EEEEEE--
T ss_pred             ehhhhcCccccceEEEEecccCCCHHHHHHHHcc---cCCCcEEEEecCc
Confidence             123333   3679999999865  457776544   4779999998743

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

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=91.09  E-value=2.5  Score=37.65  Aligned_cols=115  Identities=19%  Similarity=0.167  Sum_probs=58.9

Q ss_pred             CceEEEEEeCCCCchh---H----HHhhccCCCCCCCceEEEEecchhHHhhcCCCceEecCCCCHHHHHHHHHHhhcCC
Q 039644           67 RMKVLIVFDDVTCFSQ---L----ESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEMEALEYHHALELFSQHAFKR  139 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~~---~----~~l~~~~~~~~~~~~iivTtR~~~~~~~~~~~~~~~l~~l~~~ea~~lf~~~~~~~  139 (192)
                      +.+.|++||......+   -    ..+...+.  ..++.+|+||..............+.-..+..++. .+...+.+..
T Consensus       406 ~~~sLvLlDE~~~GtDp~eg~ala~aile~l~--~~~~~vIitTH~~el~~~~~~~~~v~~~~~~~d~~-~l~~~Ykl~~  482 (782)
T PRK00409        406 DKNSLVLFDELGAGTDPDEGAALAISILEYLR--KRGAKIIATTHYKELKALMYNREGVENASVEFDEE-TLRPTYRLLI  482 (782)
T ss_pred             CcCcEEEecCCCCCCCHHHHHHHHHHHHHHHH--HCCCEEEEECChHHHHHHHhcCCCeEEEEEEEecC-cCcEEEEEee
Confidence            5778999999975433   1    22222222  24678999999877665542211111111111110 1111111111


Q ss_pred             CCCCccHHHHHHHHHHHhCCCchHHHHHHHHhccCCHHHHHHHHHHHHh
Q 039644          140 NHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKREKEVWESAIDKLQR  188 (192)
Q Consensus       140 ~~~~~~~~~~~~~i~~~~~g~Plai~~~~~~l~~~~~~~w~~~l~~l~~  188 (192)
                      ..+   -..++-.|++.+ |+|-.+.--|..+-.......++++++++.
T Consensus       483 G~~---g~S~a~~iA~~~-Glp~~ii~~A~~~~~~~~~~~~~li~~l~~  527 (782)
T PRK00409        483 GIP---GKSNAFEIAKRL-GLPENIIEEAKKLIGEDKEKLNELIASLEE  527 (782)
T ss_pred             CCC---CCcHHHHHHHHh-CcCHHHHHHHHHHHhhhhhHHHHHHHHHHH
Confidence            111   134566677665 888888888876655455566666666543

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=91.07  E-value=1.3  Score=39.60  Aligned_cols=67  Identities=16%  Similarity=0.236  Sum_probs=44.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC---cCchHHHHhhcCCceE-EEEEeC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV---MPYIDLNFRRLSRMKV-LIVFDD   76 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---~~~~~~l~~~l~~~~~-LlVlDd   76 (192)
                      +|||.||+.++..+-...+..+-++           +.++..  ...+.+.++.   .+....|-+.++.++| ++.||+
T Consensus       602 vGKt~lAkaLA~~~Fgse~~~IriD-----------mse~~e--vskligsp~gyvG~e~gg~LteavrrrP~sVVLfde  668 (898)
T KOG1051|consen  602 VGKTELAKALAEYVFGSEENFIRLD-----------MSEFQE--VSKLIGSPPGYVGKEEGGQLTEAVKRRPYSVVLFEE  668 (898)
T ss_pred             hhHHHHHHHHHHHHcCCccceEEec-----------hhhhhh--hhhccCCCcccccchhHHHHHHHHhcCCceEEEEec
Confidence            6999999999998855555555554           333333  3334344333   3366788888888876 788899


Q ss_pred             CCCc
Q 039644           77 VTCF   80 (192)
Q Consensus        77 v~~~   80 (192)
                      ++.-
T Consensus       669 IEkA  672 (898)
T KOG1051|consen  669 IEKA  672 (898)
T ss_pred             hhhc
Confidence            9854

>PRK05541 adenylylsulfate kinase; Provisional

Probab=91.05  E-value=0.25  Score=35.12  Aligned_cols=25  Identities=28%  Similarity=0.642  Sum_probs=21.1

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +||||+|+.++..+...+...++++
T Consensus        18 sGKst~a~~l~~~l~~~~~~~~~~~   42 (176)
T PRK05541         18 SGKTTIAKALYERLKLKYSNVIYLD   42 (176)
T ss_pred             CCHHHHHHHHHHHHHHcCCcEEEEe
Confidence            6999999999999887777777764

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

Probab=91.04  E-value=0.16  Score=40.09  Aligned_cols=25  Identities=20%  Similarity=0.191  Sum_probs=20.4

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +||||||.+++......-...+|++
T Consensus        66 sGKTtLal~~~~~~~~~g~~~vyId   90 (325)
T cd00983          66 SGKTTLALHAIAEAQKLGGTVAFID   90 (325)
T ss_pred             CCHHHHHHHHHHHHHHcCCCEEEEC
Confidence            6999999999987655556778887

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=91.03  E-value=0.14  Score=36.49  Aligned_cols=113  Identities=13%  Similarity=0.112  Sum_probs=55.3

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC---cC----chHHHHhhcCCceEEEE
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV---MP----YIDLNFRRLSRMKVLIV   73 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---~~----~~~~l~~~l~~~~~LlV   73 (192)
                      +|||++|..++.+...   ..+++....      ..-.+....+.......+..   .+    +...+..... ..-+++
T Consensus        12 sGKS~~a~~l~~~~~~---~~~~iat~~------~~~~e~~~ri~~h~~~R~~~w~t~E~~~~l~~~i~~~~~-~~~~Vl   81 (170)
T PRK05800         12 SGKSRFAERLAAQSGL---QVLYIATAQ------PFDDEMAARIAHHRQRRPAHWQTVEEPLDLAELLRADAA-PGRCVL   81 (170)
T ss_pred             ccHHHHHHHHHHHcCC---CcEeCcCCC------CChHHHHHHHHHHHhcCCCCCeEecccccHHHHHHhhcC-CCCEEE
Confidence            6999999999887532   234443211      22334445554443332222   22    2222322233 233788


Q ss_pred             EeCCCCc----------hhH----HHhhccCCCCCCCceEEEEecchhHHhhcCCCceEecCCCCHHHHHHHHHHhhc
Q 039644           74 FDDVTCF----------SQL----ESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEMEALEYHHALELFSQHAF  137 (192)
Q Consensus        74 lDdv~~~----------~~~----~~l~~~~~~~~~~~~iivTtR~~~~~~~~~~~~~~~l~~l~~~ea~~lf~~~~~  137 (192)
                      +|.+...          ..|    ..+...+.  ..+..+|+++..            ...+..+.+.....|....+
T Consensus        82 ID~Lt~~~~n~l~~~~~~~~~~~l~~li~~L~--~~~~tvVlVs~E------------vg~g~vp~~~~~r~~~d~lG  145 (170)
T PRK05800         82 VDCLTTWVTNLLFEEGEEAIAAEIDALLAALQ--QLPAKIILVTNE------------VGMGIVPEYRLGRHFRDIAG  145 (170)
T ss_pred             ehhHHHHHHHHhcccchHHHHHHHHHHHHHHH--cCCCCEEEEEcC------------CcccccCCCHHHHHHHHHHH
Confidence            8887422          111    22333332  234456777643            33455555666666766553

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=90.70  E-value=0.97  Score=36.00  Aligned_cols=94  Identities=10%  Similarity=0.033  Sum_probs=52.8

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHH----HHHHHHhcCCCC-cCchHHHHhhcCCceEEEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQ----KLLSNILKDKNV-MPYIDLNFRRLSRMKVLIVFD   75 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~----~l~~~~~~~~~~-~~~~~~l~~~l~~~~~LlVlD   75 (192)
                      +||||+...+...+.......++.. -        +..++..    .+..+.. -+.. ......++..++..+=.|++|
T Consensus       133 SGKTT~l~al~~~i~~~~~~~i~ti-E--------dp~E~~~~~~~~~i~q~e-vg~~~~~~~~~l~~~lr~~pd~i~vg  202 (343)
T TIGR01420       133 SGKSTTLASMIDYINKNAAGHIITI-E--------DPIEYVHRNKRSLINQRE-VGLDTLSFANALRAALREDPDVILIG  202 (343)
T ss_pred             CCHHHHHHHHHHhhCcCCCCEEEEE-c--------CChhhhccCccceEEccc-cCCCCcCHHHHHHHhhccCCCEEEEe
Confidence            5999999999988766655666653 1        1111110    0000000 0111 225566777888899999999


Q ss_pred             CCCCchhHHHhhccCCCCCCCceEEEEecchh
Q 039644           76 DVTCFSQLESLMGSLDWLTPVSRIILTTRNKQ  107 (192)
Q Consensus        76 dv~~~~~~~~l~~~~~~~~~~~~iivTtR~~~  107 (192)
                      .+.+...+......   ...|..++.|....+
T Consensus       203 Eird~~~~~~~l~a---a~tGh~v~~T~Ha~~  231 (343)
T TIGR01420       203 EMRDLETVELALTA---AETGHLVFGTLHTNS  231 (343)
T ss_pred             CCCCHHHHHHHHHH---HHcCCcEEEEEcCCC
Confidence            99987765543332   123444555554433

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.

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=90.60  E-value=0.85  Score=35.13  Aligned_cols=77  Identities=12%  Similarity=0.100  Sum_probs=42.9

Q ss_pred             CchhHHHHHHHHHhh----CCCcceEEEeeccccccCCCChHHHHHHHHHHHhcC--------CCC---cC-----chHH
Q 039644            1 IGKTAIARAIFDKIS----GDFECSCFLENVREESQRPGGLACLRQKLLSNILKD--------KNV---MP-----YIDL   60 (192)
Q Consensus         1 iGKTtLa~~~~~~~~----~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~--------~~~---~~-----~~~~   60 (192)
                      +|||+|+..++++..    .+-+.++++- +++..   ....++...+...-.-.        .++   ..     ..-.
T Consensus        80 vGKt~L~~~i~~~~~~~~~~~~~v~V~~~-IGeR~---rev~e~~~~~~~~~~l~~tv~v~~t~~~~~~~r~~a~~~a~a  155 (276)
T cd01135          80 LPHNELAAQIARQAGVVGEEENFAVVFAA-MGITM---EDARFFKDDFEETGALERVVLFLNLANDPTIERIITPRMALT  155 (276)
T ss_pred             CChhHHHHHHHHhhhccccCCCCEEEEEE-ecccc---HHHHHHHHHhhhcCCcceEEEEEecCCCCHHHHHHHHHHHHH
Confidence            699999999988643    2224556654 43321   35666666665431100        010   00     2222


Q ss_pred             HHhhc---CCceEEEEEeCCCCch
Q 039644           61 NFRRL---SRMKVLIVFDDVTCFS   81 (192)
Q Consensus        61 l~~~l---~~~~~LlVlDdv~~~~   81 (192)
                      +.+++   .+++.|+++||+....
T Consensus       156 iAEyfrd~~g~~VLl~~D~ltr~A  179 (276)
T cd01135         156 TAEYLAYEKGKHVLVILTDMTNYA  179 (276)
T ss_pred             HHHHHHhccCCeEEEEEcChhHHH
Confidence            44444   3689999999996543

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.

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=90.51  E-value=0.85  Score=37.73  Aligned_cols=76  Identities=18%  Similarity=0.197  Sum_probs=42.2

Q ss_pred             CchhHHHHHHHHHhhCCCc-ceEEEeeccccccCCCChHHHHHHHHHHHhc--------CCCC--cC------chHHHHh
Q 039644            1 IGKTAIARAIFDKISGDFE-CSCFLENVREESQRPGGLACLRQKLLSNILK--------DKNV--MP------YIDLNFR   63 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~-~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~--------~~~~--~~------~~~~l~~   63 (192)
                      +|||+|+.+++........ .+++. .+++-.   ..+.+++..+...-.-        ..++  ..      ..-.+.+
T Consensus       154 ~GKt~L~~~~~~~~~~~~~~v~V~a-lIGER~---rEv~ef~~~~~~~~~l~rtvvV~atsd~p~~~R~~a~~~a~tiAE  229 (461)
T TIGR01039       154 VGKTVLIQELINNIAKEHGGYSVFA-GVGERT---REGNDLYHEMKESGVIDKTALVYGQMNEPPGARMRVALTGLTMAE  229 (461)
T ss_pred             CChHHHHHHHHHHHHhcCCCeEEEE-EecCCc---hHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            6999999999987654433 34443 343321   3466666666432110        0011  00      2223444


Q ss_pred             hc---CCceEEEEEeCCCCc
Q 039644           64 RL---SRMKVLIVFDDVTCF   80 (192)
Q Consensus        64 ~l---~~~~~LlVlDdv~~~   80 (192)
                      ++   ++++.|+++||+...
T Consensus       230 yfrd~~G~~VLll~DslTR~  249 (461)
T TIGR01039       230 YFRDEQGQDVLLFIDNIFRF  249 (461)
T ss_pred             HHHHhcCCeeEEEecchhHH
Confidence            44   457999999999643

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.

>PTZ00202 tuzin; Provisional

Probab=90.49  E-value=3.5  Score=34.35  Aligned_cols=121  Identities=12%  Similarity=0.082  Sum_probs=68.8

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC--cCchHHHHhhc-----C-CceEEE
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV--MPYIDLNFRRL-----S-RMKVLI   72 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--~~~~~~l~~~l-----~-~~~~Ll   72 (192)
                      +|||||++.+.....    ...++.+.       .+..+++..++..++.....  .++...+.+.+     . +++.+|
T Consensus       297 ~GKTTLlR~~~~~l~----~~qL~vNp-------rg~eElLr~LL~ALGV~p~~~k~dLLrqIqeaLl~~~~e~GrtPVL  365 (550)
T PTZ00202        297 CGKSSLCRSAVRKEG----MPAVFVDV-------RGTEDTLRSVVKALGVPNVEACGDLLDFISEACRRAKKMNGETPLL  365 (550)
T ss_pred             CCHHHHHHHHHhcCC----ceEEEECC-------CCHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHHHHHhCCCCEEE
Confidence            699999999997664    22444333       35689999999999864332  12333333333     2 455555


Q ss_pred             EEeCCCCchhHHHh---hccCCCCCCCceEEEEecchhHHhhc---CCCceEecCCCCHHHHHHHHH
Q 039644           73 VFDDVTCFSQLESL---MGSLDWLTPVSRIILTTRNKQVLRNW---GVSKIYEMEALEYHHALELFS  133 (192)
Q Consensus        73 VlDdv~~~~~~~~l---~~~~~~~~~~~~iivTtR~~~~~~~~---~~~~~~~l~~l~~~ea~~lf~  133 (192)
                      |+-= .+.+.+...   .-.+-....-|+|++---.+......   +.-..|-+++++..+|.....
T Consensus       366 II~l-reg~~l~rvyne~v~la~drr~ch~v~evpleslt~~~~~lprldf~~vp~fsr~qaf~y~~  431 (550)
T PTZ00202        366 VLKL-REGSSLQRVYNEVVALACDRRLCHVVIEVPLESLTIANTLLPRLDFYLVPNFSRSQAFAYTQ  431 (550)
T ss_pred             EEEe-cCCCcHHHHHHHHHHHHccchhheeeeeehHhhcchhcccCccceeEecCCCCHHHHHHHHh
Confidence            5543 322222111   11122234568899877665543332   223467788999988776543

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

Probab=90.45  E-value=1.7  Score=38.73  Aligned_cols=24  Identities=8%  Similarity=0.191  Sum_probs=18.8

Q ss_pred             CCCceEecCCCCHHHHHHHHHHhh
Q 039644          113 GVSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus       113 ~~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      +....+.+.+++.++-.++..++.
T Consensus       483 ~R~~ii~~~~~t~eek~~Ia~~~L  506 (784)
T PRK10787        483 DRMEVIRLSGYTEDEKLNIAKRHL  506 (784)
T ss_pred             cceeeeecCCCCHHHHHHHHHHhh
Confidence            345788999999999888876655

>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=90.43  E-value=0.2  Score=33.05  Aligned_cols=14  Identities=21%  Similarity=0.636  Sum_probs=12.9

Q ss_pred             CchhHHHHHHHHHh
Q 039644            1 IGKTAIARAIFDKI   14 (192)
Q Consensus         1 iGKTtLa~~~~~~~   14 (192)
                      +||||+|+.+++++
T Consensus        10 sGKST~a~~La~~~   23 (121)
T PF13207_consen   10 SGKSTLAKELAERL   23 (121)
T ss_dssp             SSHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH
Confidence            69999999999976

...

>COG1158 Rho Transcription termination factor [Transcription]

Probab=90.42  E-value=0.67  Score=36.65  Aligned_cols=75  Identities=21%  Similarity=0.382  Sum_probs=48.3

Q ss_pred             CchhHHHHHHHHHhhCCC-cceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC------cC----chHHHHhhcC-Cc
Q 039644            1 IGKTAIARAIFDKISGDF-ECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV------MP----YIDLNFRRLS-RM   68 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F-~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~------~~----~~~~l~~~l~-~~   68 (192)
                      .|||+|.+.+++.+..+. ++..||-.+.+   .|.-+.++++..--++....-+      ..    .++.-++... ++
T Consensus       184 aGKT~lLq~IA~aIt~N~Pe~~LiVLLIDE---RPEEVTdmqrsV~geViaSTFDepp~~HvqVAE~viEkAKRlVE~~k  260 (422)
T COG1158         184 AGKTTLLQNIANAITTNHPECELIVLLIDE---RPEEVTDMQRSVKGEVVASTFDEPPSRHVQVAEMVIEKAKRLVEHGK  260 (422)
T ss_pred             CCchHHHHHHHHHHhcCCCceEEEEEEecC---CchHHHHHHHhhcceEEeecCCCcchhhHHHHHHHHHHHHHHHHcCC
Confidence            499999999999887666 57788776533   3456777766665333222111      11    4455555554 56


Q ss_pred             eEEEEEeCCC
Q 039644           69 KVLIVFDDVT   78 (192)
Q Consensus        69 ~~LlVlDdv~   78 (192)
                      ...|.||.+.
T Consensus       261 DVVILLDSIT  270 (422)
T COG1158         261 DVVILLDSIT  270 (422)
T ss_pred             cEEEEehhHH
Confidence            8889999884

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=90.30  E-value=0.8  Score=37.97  Aligned_cols=75  Identities=20%  Similarity=0.119  Sum_probs=42.7

Q ss_pred             CchhHHHHHHHHHhhCC-CcceEEEeeccccccCCCChHHHHHHHHHHHhc--------CCCC--cC------chHHHHh
Q 039644            1 IGKTAIARAIFDKISGD-FECSCFLENVREESQRPGGLACLRQKLLSNILK--------DKNV--MP------YIDLNFR   63 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~-F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~--------~~~~--~~------~~~~l~~   63 (192)
                      +|||+|+.+++.....+ -+.+++.. +++-   ...+.++...+...-.-        ..++  ..      ..-.+.+
T Consensus       154 ~GKt~Ll~~~~~~~~~~~~dv~V~~l-iGER---~rEv~ef~~~~~~~~~l~rsvvv~atsd~~~~~R~~a~~~a~tiAE  229 (461)
T PRK12597        154 VGKTVLMMELIFNISKQHSGSSVFAG-VGER---SREGHELYHEMKESGVLDKTVMVYGQMNEPPGARMRVVLTGLTIAE  229 (461)
T ss_pred             CChhHHHHHHHHHHHhhCCCEEEEEc-CCcc---hHHHHHHHHHHHhcCCcceeEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence            69999999999976533 34555553 4331   13456666655443110        0011  00      2333445


Q ss_pred             hc---CCceEEEEEeCCCC
Q 039644           64 RL---SRMKVLIVFDDVTC   79 (192)
Q Consensus        64 ~l---~~~~~LlVlDdv~~   79 (192)
                      ++   .+++.|+++||+..
T Consensus       230 yfrd~~G~~VLl~~DslTR  248 (461)
T PRK12597        230 YLRDEEKEDVLLFIDNIFR  248 (461)
T ss_pred             HHHHhcCCceEEEeccchH
Confidence            55   37899999999943

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=90.29  E-value=0.65  Score=35.85  Aligned_cols=72  Identities=17%  Similarity=0.105  Sum_probs=43.4

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHH-H---hcCCCC-cC----chHHHHhhcCCceEE
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSN-I---LKDKNV-MP----YIDLNFRRLSRMKVL   71 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~-~---~~~~~~-~~----~~~~l~~~l~~~~~L   71 (192)
                      +||||+|.+++-.....-...+|++.-+.     +....+. .+... +   .-..+. .+    ++..+.......--|
T Consensus        71 sGKT~lal~~~~~aq~~g~~a~fIDtE~~-----l~p~r~~-~l~~~~~d~l~v~~~~~~e~q~~i~~~~~~~~~~~i~L  144 (279)
T COG0468          71 SGKTTLALQLVANAQKPGGKAAFIDTEHA-----LDPERAK-QLGVDLLDNLLVSQPDTGEQQLEIAEKLARSGAEKIDL  144 (279)
T ss_pred             cchhhHHHHHHHHhhcCCCeEEEEeCCCC-----CCHHHHH-HHHHhhhcceeEecCCCHHHHHHHHHHHHHhccCCCCE
Confidence            59999999998877666668899984333     3444433 33333 2   111121 11    444444444444569


Q ss_pred             EEEeCCC
Q 039644           72 IVFDDVT   78 (192)
Q Consensus        72 lVlDdv~   78 (192)
                      +|+|.+.
T Consensus       145 vVVDSva  151 (279)
T COG0468         145 LVVDSVA  151 (279)
T ss_pred             EEEecCc
Confidence            9999995

>TIGR01069 mutS2 MutS2 family protein

Probab=90.27  E-value=0.67  Score=41.05  Aligned_cols=114  Identities=17%  Similarity=0.174  Sum_probs=59.1

Q ss_pred             CceEEEEEeCCCCchh---HH----HhhccCCCCCCCceEEEEecchhHHhhcC-CCceEecCCCCHHHHHHHHHHhhcC
Q 039644           67 RMKVLIVFDDVTCFSQ---LE----SLMGSLDWLTPVSRIILTTRNKQVLRNWG-VSKIYEMEALEYHHALELFSQHAFK  138 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~~---~~----~l~~~~~~~~~~~~iivTtR~~~~~~~~~-~~~~~~l~~l~~~ea~~lf~~~~~~  138 (192)
                      +.+-|++||.+-...+   -.    .+...+.  ..|+.+|+||.......... ...+.. ..+..++. .+-..+-+.
T Consensus       401 ~~~sLvLlDE~g~GtD~~eg~ala~aiLe~l~--~~g~~viitTH~~eL~~~~~~~~~v~~-~~~~~d~~-~l~p~Ykl~  476 (771)
T TIGR01069       401 TENSLVLFDELGAGTDPDEGSALAISILEYLL--KQNAQVLITTHYKELKALMYNNEGVEN-ASVLFDEE-TLSPTYKLL  476 (771)
T ss_pred             CCCcEEEecCCCCCCCHHHHHHHHHHHHHHHH--hcCCEEEEECChHHHHHHhcCCCCeEE-eEEEEcCC-CCceEEEEC
Confidence            5789999999975432   22    2222222  24678999999877654431 111111 11111110 110011111


Q ss_pred             CCCCCccHHHHHHHHHHHhCCCchHHHHHHHHhccCCHHHHHHHHHHHHh
Q 039644          139 RNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKREKEVWESAIDKLQR  188 (192)
Q Consensus       139 ~~~~~~~~~~~~~~i~~~~~g~Plai~~~~~~l~~~~~~~w~~~l~~l~~  188 (192)
                      ...+   -..++-.|++.+ |+|-.|.--|..+........++++++++.
T Consensus       477 ~G~~---g~S~a~~iA~~~-Glp~~ii~~A~~~~~~~~~~~~~li~~L~~  522 (771)
T TIGR01069       477 KGIP---GESYAFEIAQRY-GIPHFIIEQAKTFYGEFKEEINVLIEKLSA  522 (771)
T ss_pred             CCCC---CCcHHHHHHHHh-CcCHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            1111   134566677665 888888888876665455566666666653

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.

>cd01394 radB RadB

Probab=90.19  E-value=0.96  Score=33.29  Aligned_cols=25  Identities=24%  Similarity=0.339  Sum_probs=19.4

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +|||+||.+++......-..++|++
T Consensus        30 sGKT~l~~~~a~~~~~~g~~v~yi~   54 (218)
T cd01394          30 TGKTNIAIQLAVETAGQGKKVAYID   54 (218)
T ss_pred             CCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            6999999999997654445667886

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

>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=90.13  E-value=0.48  Score=37.32  Aligned_cols=25  Identities=20%  Similarity=0.263  Sum_probs=20.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +||||||.+++......-...+|++
T Consensus        64 sGKttLaL~~ia~~q~~g~~~a~ID   88 (322)
T PF00154_consen   64 SGKTTLALHAIAEAQKQGGICAFID   88 (322)
T ss_dssp             SSHHHHHHHHHHHHHHTT-EEEEEE
T ss_pred             CchhhhHHHHHHhhhcccceeEEec
Confidence            6999999999998765556788987

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 ....

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

Probab=90.09  E-value=0.6  Score=39.87  Aligned_cols=18  Identities=39%  Similarity=0.545  Sum_probs=15.4

Q ss_pred             CchhHHHHHHHHHhhCCC
Q 039644            1 IGKTAIARAIFDKISGDF   18 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F   18 (192)
                      +|||.||+.++.+..-.|
T Consensus       234 CGKT~lA~AiAgel~vPf  251 (802)
T KOG0733|consen  234 CGKTSLANAIAGELGVPF  251 (802)
T ss_pred             ccHHHHHHHHhhhcCCce
Confidence            699999999999876554

>PRK10865 protein disaggregation chaperone; Provisional

Probab=90.08  E-value=3.9  Score=36.88  Aligned_cols=16  Identities=38%  Similarity=0.615  Sum_probs=13.8

Q ss_pred             CchhHHHHHHHHHhhC
Q 039644            1 IGKTAIARAIFDKISG   16 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~   16 (192)
                      +|||++|+.++.++..
T Consensus       210 vGKT~l~~~la~~i~~  225 (857)
T PRK10865        210 VGKTAIVEGLAQRIIN  225 (857)
T ss_pred             CCHHHHHHHHHHHhhc
Confidence            6999999999998643

>TIGR02012 tigrfam_recA protein RecA

Probab=90.06  E-value=0.18  Score=39.68  Aligned_cols=25  Identities=20%  Similarity=0.268  Sum_probs=19.7

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +||||||.+++......-..++|++
T Consensus        66 sGKTtLaL~~~~~~~~~g~~v~yId   90 (321)
T TIGR02012        66 SGKTTLALHAIAEAQKAGGTAAFID   90 (321)
T ss_pred             CCHHHHHHHHHHHHHHcCCcEEEEc
Confidence            6999999999887655545677886

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.

>PRK09354 recA recombinase A; Provisional

Probab=89.82  E-value=0.24  Score=39.42  Aligned_cols=25  Identities=20%  Similarity=0.268  Sum_probs=20.5

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +||||||.+++......-...+|++
T Consensus        71 sGKTtLal~~~~~~~~~G~~~~yId   95 (349)
T PRK09354         71 SGKTTLALHAIAEAQKAGGTAAFID   95 (349)
T ss_pred             CCHHHHHHHHHHHHHHcCCcEEEEC
Confidence            6999999999987655556778887

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=89.78  E-value=0.91  Score=37.61  Aligned_cols=76  Identities=20%  Similarity=0.207  Sum_probs=42.5

Q ss_pred             CchhHHHHHHHHHhhCCCc-ceEEEeeccccccCCCChHHHHHHHHHHHhcC--------CCC--cC------chHHHHh
Q 039644            1 IGKTAIARAIFDKISGDFE-CSCFLENVREESQRPGGLACLRQKLLSNILKD--------KNV--MP------YIDLNFR   63 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~-~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~--------~~~--~~------~~~~l~~   63 (192)
                      +|||+|+.+++.......+ .+++. .+++-   ...+.+++..++..-.-.        .+.  ..      ..-.+.+
T Consensus       155 vGKt~Ll~~i~~~~~~~~~~v~V~~-liGER---~rEv~efi~~~~~~~~l~rsvvV~atsd~p~~~r~~a~~~a~tiAE  230 (463)
T PRK09280        155 VGKTVLIQELINNIAKEHGGYSVFA-GVGER---TREGNDLYHEMKESGVLDKTALVFGQMNEPPGARLRVALTGLTMAE  230 (463)
T ss_pred             CChhHHHHHHHHHHHhcCCCEEEEE-EeccC---cHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            6999999999887654433 33433 24331   145666666665431100        011  00      2223444


Q ss_pred             hc---CCceEEEEEeCCCCc
Q 039644           64 RL---SRMKVLIVFDDVTCF   80 (192)
Q Consensus        64 ~l---~~~~~LlVlDdv~~~   80 (192)
                      ++   .+++.|+++||+...
T Consensus       231 yfrd~~G~~VLll~DslTR~  250 (463)
T PRK09280        231 YFRDVEGQDVLLFIDNIFRF  250 (463)
T ss_pred             HHHHhcCCceEEEecchHHH
Confidence            44   568999999999543

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=89.75  E-value=1.3  Score=35.41  Aligned_cols=43  Identities=9%  Similarity=0.053  Sum_probs=24.9

Q ss_pred             CchhHHHHHHHHHh--hCC----CcceEEEeeccccccCCCChHHHHHHHHHHHh
Q 039644            1 IGKTAIARAIFDKI--SGD----FECSCFLENVREESQRPGGLACLRQKLLSNIL   49 (192)
Q Consensus         1 iGKTtLa~~~~~~~--~~~----F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~   49 (192)
                      +|||+|+.+++-..  ...    -..++|++.-..     +....+.+ +.+.+.
T Consensus       137 sGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~t-----F~peRl~~-ia~~~g  185 (344)
T PLN03187        137 SGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGT-----FRPDRIVP-IAERFG  185 (344)
T ss_pred             CChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCC-----CCHHHHHH-HHHHcC
Confidence            69999999987532  211    136788873222     45555543 444443

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=89.65  E-value=1.4  Score=35.59  Aligned_cols=70  Identities=7%  Similarity=0.149  Sum_probs=39.0

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCc-----CchHHHHhhcC-CceEEEEE
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVM-----PYIDLNFRRLS-RMKVLIVF   74 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~-----~~~~~l~~~l~-~~~~LlVl   74 (192)
                      +|||||+.+++..+...-..++|++. .      .....+... .+.+....+..     .....+...+. .++-++|+
T Consensus        93 ~GKStLllq~a~~~a~~g~~VlYvs~-E------Es~~qi~~R-a~rlg~~~~~l~l~~e~~le~I~~~i~~~~~~lVVI  164 (372)
T cd01121          93 IGKSTLLLQVAARLAKRGGKVLYVSG-E------ESPEQIKLR-ADRLGISTENLYLLAETNLEDILASIEELKPDLVII  164 (372)
T ss_pred             CCHHHHHHHHHHHHHhcCCeEEEEEC-C------cCHHHHHHH-HHHcCCCcccEEEEccCcHHHHHHHHHhcCCcEEEE
Confidence            69999999999976655456777762 1      122222211 22332211111     13344444443 36779999


Q ss_pred             eCCC
Q 039644           75 DDVT   78 (192)
Q Consensus        75 Ddv~   78 (192)
                      |.+.
T Consensus       165 DSIq  168 (372)
T cd01121         165 DSIQ  168 (372)
T ss_pred             cchH
Confidence            9985

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.

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=89.61  E-value=14  Score=32.47  Aligned_cols=128  Identities=12%  Similarity=0.155  Sum_probs=75.8

Q ss_pred             CchhHHHHHHHHHhh-----CCCcce--EEEeeccccccCCCChHHHHHHHHHHHhcCCCC-cCchHHHHhhcC-----C
Q 039644            1 IGKTAIARAIFDKIS-----GDFECS--CFLENVREESQRPGGLACLRQKLLSNILKDKNV-MPYIDLNFRRLS-----R   67 (192)
Q Consensus         1 iGKTtLa~~~~~~~~-----~~F~~~--~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~~~~~l~~~l~-----~   67 (192)
                      +|||..+..|.+.++     ..-+..  +.+..+.-     ....+++..|...+.+.... ....+.+..++.     .
T Consensus       433 tGKT~tV~~Vm~~Lq~~s~~~e~p~f~yveINgm~l-----~~~~~~Y~~I~~~lsg~~~~~~~al~~L~~~f~~~k~~~  507 (767)
T KOG1514|consen  433 TGKTATVLEVMKELQTSSAQKELPKFDYVEINGLRL-----ASPREIYEKIWEALSGERVTWDAALEALNFRFTVPKPKR  507 (767)
T ss_pred             CCceehHHHHHHHHHHHHhhcCCCCccEEEEcceee-----cCHHHHHHHHHHhcccCcccHHHHHHHHHHhhccCCCCC
Confidence            599999999999532     112222  33433322     46889999999988877655 335566666664     3


Q ss_pred             ceEEEEEeCCCCc-----hhHHHhhccCCCCCCCceEEEEecc--h-----h----HHhhcCCCceEecCCCCHHHHHHH
Q 039644           68 MKVLIVFDDVTCF-----SQLESLMGSLDWLTPVSRIILTTRN--K-----Q----VLRNWGVSKIYEMEALEYHHALEL  131 (192)
Q Consensus        68 ~~~LlVlDdv~~~-----~~~~~l~~~~~~~~~~~~iivTtR~--~-----~----~~~~~~~~~~~~l~~l~~~ea~~l  131 (192)
                      ..+++++|+++..     +.+..|... | ...++|++|.+=.  -     .    +....+ -..+..++.++.+..++
T Consensus       508 ~~~VvLiDElD~Lvtr~QdVlYn~fdW-p-t~~~sKLvvi~IaNTmdlPEr~l~nrvsSRlg-~tRi~F~pYth~qLq~I  584 (767)
T KOG1514|consen  508 STTVVLIDELDILVTRSQDVLYNIFDW-P-TLKNSKLVVIAIANTMDLPERLLMNRVSSRLG-LTRICFQPYTHEQLQEI  584 (767)
T ss_pred             CCEEEEeccHHHHhcccHHHHHHHhcC-C-cCCCCceEEEEecccccCHHHHhccchhhhcc-ceeeecCCCCHHHHHHH
Confidence            5789999999743     224555432 2 3466777665411  0     0    111111 23466777777777776


Q ss_pred             HHHhh
Q 039644          132 FSQHA  136 (192)
Q Consensus       132 f~~~~  136 (192)
                      ...+.
T Consensus       585 i~~RL  589 (767)
T KOG1514|consen  585 ISARL  589 (767)
T ss_pred             HHHhh
Confidence            65554

>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=89.42  E-value=0.33  Score=32.98  Aligned_cols=15  Identities=20%  Similarity=0.541  Sum_probs=12.8

Q ss_pred             CchhHHHHHHHHHhh
Q 039644            1 IGKTAIARAIFDKIS   15 (192)
Q Consensus         1 iGKTtLa~~~~~~~~   15 (192)
                      +||||+|+.+.....
T Consensus        10 sGKSt~a~~l~~~~~   24 (143)
T PF13671_consen   10 SGKSTLAKRLAKRLG   24 (143)
T ss_dssp             SSHHHHHHHHHHHST
T ss_pred             CCHHHHHHHHHHHCC
Confidence            699999999987654

...

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=89.37  E-value=1.6  Score=34.36  Aligned_cols=72  Identities=13%  Similarity=0.166  Sum_probs=37.8

Q ss_pred             CchhHHHHHHHHHh--hC----CCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-cC---------------ch
Q 039644            1 IGKTAIARAIFDKI--SG----DFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV-MP---------------YI   58 (192)
Q Consensus         1 iGKTtLa~~~~~~~--~~----~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~---------------~~   58 (192)
                      +|||+|+.+++-..  ..    .=..++|++.-..     +....+. .+.+.+..+.+. .+               .+
T Consensus       107 sGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~-----f~~eRi~-~~a~~~g~d~~~~l~~i~~~~~~~~e~~~~~l  180 (313)
T TIGR02238       107 CGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGT-----FRPDRIR-AIAERFGVDPDAVLDNILYARAYTSEHQMELL  180 (313)
T ss_pred             CCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCC-----CCHHHHH-HHHHHcCCChHHhcCcEEEecCCCHHHHHHHH
Confidence            69999999987532  21    1136788873222     4444444 344444332211 11               22


Q ss_pred             HHHHhhcC-CceEEEEEeCCC
Q 039644           59 DLNFRRLS-RMKVLIVFDDVT   78 (192)
Q Consensus        59 ~~l~~~l~-~~~~LlVlDdv~   78 (192)
                      ..+...+. .+.-|+|+|.+.
T Consensus       181 ~~l~~~i~~~~~~LvVIDSis  201 (313)
T TIGR02238       181 DYLAAKFSEEPFRLLIVDSIM  201 (313)
T ss_pred             HHHHHHhhccCCCEEEEEcch
Confidence            33333333 345589999985

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.

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=89.34  E-value=1.8  Score=33.96  Aligned_cols=26  Identities=15%  Similarity=0.213  Sum_probs=18.7

Q ss_pred             CchhHHHHHHHHHhhCCC------cceEEEee
Q 039644            1 IGKTAIARAIFDKISGDF------ECSCFLEN   26 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F------~~~~wv~~   26 (192)
                      +|||+|+.+++.......      ..++|++.
T Consensus       113 sGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~t  144 (317)
T PRK04301        113 SGKTQICHQLAVNVQLPEEKGGLEGKAVYIDT  144 (317)
T ss_pred             CCHhHHHHHHHHHhccccccCCCCceEEEEeC
Confidence            699999999988643221      36788873

>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=89.29  E-value=0.43  Score=33.48  Aligned_cols=25  Identities=28%  Similarity=0.287  Sum_probs=20.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +||||||+.+.+++.+.-..+.+++
T Consensus        13 sGKtTlA~~L~~~L~~~g~~~~~LD   37 (156)
T PF01583_consen   13 SGKTTLARALERRLFARGIKVYLLD   37 (156)
T ss_dssp             SSHHHHHHHHHHHHHHTTS-EEEEE
T ss_pred             CCHHHHHHHHHHHHHHcCCcEEEec
Confidence            5999999999999887766667765

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 ....

>PRK06762 hypothetical protein; Provisional

Probab=88.90  E-value=0.85  Score=31.95  Aligned_cols=14  Identities=36%  Similarity=0.677  Sum_probs=12.8

Q ss_pred             CchhHHHHHHHHHh
Q 039644            1 IGKTAIARAIFDKI   14 (192)
Q Consensus         1 iGKTtLa~~~~~~~   14 (192)
                      +||||+|+.+++.+
T Consensus        13 sGKST~A~~L~~~l   26 (166)
T PRK06762         13 SGKTTIAKQLQERL   26 (166)
T ss_pred             CCHHHHHHHHHHHh
Confidence            69999999999887

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

Probab=88.48  E-value=6.1  Score=33.10  Aligned_cols=118  Identities=17%  Similarity=0.126  Sum_probs=65.6

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||.||+.++......|-.+..-+.++..- .  .....                +...+.......++.|.+|.+++.
T Consensus       287 tGKT~lAkava~~~~~~fi~v~~~~l~sk~v-G--esek~----------------ir~~F~~A~~~~p~iiFiDEiDs~  347 (494)
T COG0464         287 TGKTLLAKAVALESRSRFISVKGSELLSKWV-G--ESEKN----------------IRELFEKARKLAPSIIFIDEIDSL  347 (494)
T ss_pred             CCHHHHHHHHHhhCCCeEEEeeCHHHhcccc-c--hHHHH----------------HHHHHHHHHcCCCcEEEEEchhhh
Confidence            5999999999997766654433322111100 0  00111                222233333577899999999642


Q ss_pred             h-------------hHHHhhccCCCCC--CCceEEEEecchhHHhhc-----CCCceEecCCCCHHHHHHHHHHhhc
Q 039644           81 S-------------QLESLMGSLDWLT--PVSRIILTTRNKQVLRNW-----GVSKIYEMEALEYHHALELFSQHAF  137 (192)
Q Consensus        81 ~-------------~~~~l~~~~~~~~--~~~~iivTtR~~~~~~~~-----~~~~~~~l~~l~~~ea~~lf~~~~~  137 (192)
                      .             ....+...+....  .+..||-+|.........     .-...+.+..-+..+..++|..+..
T Consensus       348 ~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~~v~vi~aTN~p~~ld~a~lR~gRfd~~i~v~~pd~~~r~~i~~~~~~  424 (494)
T COG0464         348 ASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLR  424 (494)
T ss_pred             hccCCCCCchHHHHHHHHHHHHhcCCCccCceEEEecCCCccccCHhhcccCccceEeecCCCCHHHHHHHHHHHhc
Confidence            1             1233333333222  333344455544433321     2245788888899999999998874

>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=88.35  E-value=2.1  Score=29.43  Aligned_cols=93  Identities=15%  Similarity=0.096  Sum_probs=46.7

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      .|||||++.++..... ..+.+++.......-. +.           +.   ......-.+.+.+-.++-++++|+..+.
T Consensus        37 sGKStLl~~l~G~~~~-~~G~i~~~~~~~i~~~-~~-----------lS---~G~~~rv~laral~~~p~illlDEP~~~  100 (144)
T cd03221          37 AGKSTLLKLIAGELEP-DEGIVTWGSTVKIGYF-EQ-----------LS---GGEKMRLALAKLLLENPNLLLLDEPTNH  100 (144)
T ss_pred             CCHHHHHHHHcCCCCC-CceEEEECCeEEEEEE-cc-----------CC---HHHHHHHHHHHHHhcCCCEEEEeCCccC
Confidence            5999999999885432 3555665421111000 00           00   0000122244455566779999999743


Q ss_pred             hh---HHHhhccCCCCCCCceEEEEecchhHHhh
Q 039644           81 SQ---LESLMGSLDWLTPVSRIILTTRNKQVLRN  111 (192)
Q Consensus        81 ~~---~~~l~~~~~~~~~~~~iivTtR~~~~~~~  111 (192)
                      -+   ...+...+...  +..|+++|........
T Consensus       101 LD~~~~~~l~~~l~~~--~~til~~th~~~~~~~  132 (144)
T cd03221         101 LDLESIEALEEALKEY--PGTVILVSHDRYFLDQ  132 (144)
T ss_pred             CCHHHHHHHHHHHHHc--CCEEEEEECCHHHHHH
Confidence            22   22332222221  2458888877665543

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.

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=88.32  E-value=1.5  Score=31.12  Aligned_cols=58  Identities=16%  Similarity=0.102  Sum_probs=32.4

Q ss_pred             HHhhcCCceEEEEEeCCCCchh---HHHhhccCCCCCCCceEEEEecchhHHhhcCCCceEec
Q 039644           61 NFRRLSRMKVLIVFDDVTCFSQ---LESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEM  120 (192)
Q Consensus        61 l~~~l~~~~~LlVlDdv~~~~~---~~~l~~~~~~~~~~~~iivTtR~~~~~~~~~~~~~~~l  120 (192)
                      +.+.+-.++-+++||...+.-+   .+.+...+.....+..||++|.+......  ..+.+.+
T Consensus       109 laral~~~p~~lllDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~sh~~~~~~~--~d~~~~l  169 (178)
T cd03247         109 LARILLQDAPIVLLDEPTVGLDPITERQLLSLIFEVLKDKTLIWITHHLTGIEH--MDKILFL  169 (178)
T ss_pred             HHHHHhcCCCEEEEECCcccCCHHHHHHHHHHHHHHcCCCEEEEEecCHHHHHh--CCEEEEE
Confidence            5555567888999999975422   22222222111235668888887765542  3444444

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.

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=88.31  E-value=1.1  Score=34.59  Aligned_cols=21  Identities=19%  Similarity=0.409  Sum_probs=15.4

Q ss_pred             CCceEEEEEeCCCCchh-HHHh
Q 039644           66 SRMKVLIVFDDVTCFSQ-LESL   86 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~~~-~~~l   86 (192)
                      .+++.|+++||+....+ +.++
T Consensus       159 ~G~~Vlvl~DslTr~A~A~rEi  180 (274)
T cd01132         159 NGKHALIIYDDLSKQAVAYRQM  180 (274)
T ss_pred             CCCCEEEEEcChHHHHHHHHHH
Confidence            47899999999976533 4444

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.

>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=88.09  E-value=0.37  Score=31.87  Aligned_cols=14  Identities=36%  Similarity=0.688  Sum_probs=12.7

Q ss_pred             CchhHHHHHHHHHh
Q 039644            1 IGKTAIARAIFDKI   14 (192)
Q Consensus         1 iGKTtLa~~~~~~~   14 (192)
                      +||||+|+++.+++
T Consensus         9 sGKtTia~~L~~~~   22 (129)
T PF13238_consen    9 SGKTTIAKELAERL   22 (129)
T ss_dssp             SSHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH
Confidence            69999999999984

...

>TIGR00602 rad24 checkpoint protein rad24

Probab=88.04  E-value=3.6  Score=35.67  Aligned_cols=48  Identities=4%  Similarity=-0.069  Sum_probs=26.6

Q ss_pred             ceEecCCCCHHHHHHHHHHhhcCCCC---CC--ccHHHHHHHHHHHhCCCchH
Q 039644          116 KIYEMEALEYHHALELFSQHAFKRNH---PD--VGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       116 ~~~~l~~l~~~ea~~lf~~~~~~~~~---~~--~~~~~~~~~i~~~~~g~Pla  163 (192)
                      ..+..++++..+....+.+.+-....   ..  ....+....|+..++|--..
T Consensus       267 ~~I~FnPia~t~l~K~L~rIl~~E~~~~~~~~~~p~~~~l~~I~~~s~GDiRs  319 (637)
T TIGR00602       267 SNISFNPIAPTIMKKFLNRIVTIEAKKNGEKIKVPKKTSVELLCQGCSGDIRS  319 (637)
T ss_pred             eEEEeCCCCHHHHHHHHHHHHHhhhhccccccccCCHHHHHHHHHhCCChHHH
Confidence            45889999999866666554422110   01  01234555666666666443

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

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=88.02  E-value=0.33  Score=34.91  Aligned_cols=45  Identities=9%  Similarity=0.054  Sum_probs=27.7

Q ss_pred             CceEEEEEeCCCCchh-------HHHhhccCCCCCCCceEEEEecchhHHhhc
Q 039644           67 RMKVLIVFDDVTCFSQ-------LESLMGSLDWLTPVSRIILTTRNKQVLRNW  112 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~~-------~~~l~~~~~~~~~~~~iivTtR~~~~~~~~  112 (192)
                      +++-|+++|......+       ...+...+.. ..++.+|++|....+....
T Consensus        77 ~~~~llllDEp~~g~d~~~~~~~~~~~l~~l~~-~~~~~iii~TH~~~l~~~~  128 (185)
T smart00534       77 TENSLVLLDELGRGTSTYDGVAIAAAVLEYLLE-KIGALTLFATHYHELTKLA  128 (185)
T ss_pred             CCCeEEEEecCCCCCCHHHHHHHHHHHHHHHHh-cCCCeEEEEecHHHHHHHh
Confidence            3789999999964322       1222222221 1356799999988766654

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

Probab=87.97  E-value=2.7  Score=37.25  Aligned_cols=21  Identities=0%  Similarity=0.080  Sum_probs=17.7

Q ss_pred             CceEecCCCCHHHHHHHHHHh
Q 039644          115 SKIYEMEALEYHHALELFSQH  135 (192)
Q Consensus       115 ~~~~~l~~l~~~ea~~lf~~~  135 (192)
                      -+.+.+++.+.++..+++...
T Consensus       341 Fq~I~v~ePs~~~~~~IL~~~  361 (758)
T PRK11034        341 FQKIDITEPSIEETVQIINGL  361 (758)
T ss_pred             CcEEEeCCCCHHHHHHHHHHH
Confidence            357999999999999998854

>PRK07261 topology modulation protein; Provisional

Probab=87.90  E-value=1.5  Score=31.10  Aligned_cols=14  Identities=29%  Similarity=0.487  Sum_probs=12.2

Q ss_pred             CchhHHHHHHHHHh
Q 039644            1 IGKTAIARAIFDKI   14 (192)
Q Consensus         1 iGKTtLa~~~~~~~   14 (192)
                      +||||||+.+....
T Consensus        11 sGKSTla~~l~~~~   24 (171)
T PRK07261         11 SGKSTLARKLSQHY   24 (171)
T ss_pred             CCHHHHHHHHHHHh
Confidence            69999999998864

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

Probab=86.86  E-value=8.2  Score=29.38  Aligned_cols=20  Identities=15%  Similarity=0.351  Sum_probs=14.1

Q ss_pred             CchhHHHHHHHHHhhCCCcc
Q 039644            1 IGKTAIARAIFDKISGDFEC   20 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~   20 (192)
                      +||++|++.+...+...+-.
T Consensus        96 tGKSSLVKA~~~e~~~~glr  115 (287)
T COG2607          96 TGKSSLVKALLNEYADEGLR  115 (287)
T ss_pred             CChHHHHHHHHHHHHhcCCe
Confidence            47888888888776665544

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=86.83  E-value=2.4  Score=33.86  Aligned_cols=26  Identities=15%  Similarity=0.238  Sum_probs=17.6

Q ss_pred             CchhHHHHHHHHHhh--CC----CcceEEEee
Q 039644            1 IGKTAIARAIFDKIS--GD----FECSCFLEN   26 (192)
Q Consensus         1 iGKTtLa~~~~~~~~--~~----F~~~~wv~~   26 (192)
                      +|||+|+..++-...  ..    -..++|++.
T Consensus       134 ~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdt  165 (342)
T PLN03186        134 TGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDT  165 (342)
T ss_pred             CCccHHHHHHHHHhhcchhhCCCCceEEEEEC
Confidence            699999998886422  11    125889884

>TIGR03324 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha

Probab=86.69  E-value=1.6  Score=36.56  Aligned_cols=73  Identities=23%  Similarity=0.264  Sum_probs=38.1

Q ss_pred             CchhHHHH-HHHHHhhCCCcc-eEEEeeccccccCCCChHHHHHHHHHHHhc--------CCCC---cC-----chHHHH
Q 039644            1 IGKTAIAR-AIFDKISGDFEC-SCFLENVREESQRPGGLACLRQKLLSNILK--------DKNV---MP-----YIDLNF   62 (192)
Q Consensus         1 iGKTtLa~-~~~~~~~~~F~~-~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~--------~~~~---~~-----~~~~l~   62 (192)
                      +|||+||. .++++...  +. .+++. +++..   ..+.++...+...-.-        ..++   ..     ..-.+.
T Consensus       173 ~GKT~Lal~~I~~q~~~--dv~~V~~~-IGeR~---rev~e~i~~l~~~~~l~~tvvV~atsd~p~~~r~~ap~~a~aiA  246 (497)
T TIGR03324       173 TGKTAIAIDTILNQKGR--NVLCIYCA-IGQRA---SAVAKVVANLREHGAMDYTIVVVTEGNDPPGLQYIAPYAATSIG  246 (497)
T ss_pred             CCHHHHHHHHHHHhcCC--CcEEEEEE-eccCc---HHHHHHHHHhhhcCCcceeEEEEeCCCCCHHHHHHHHHHHHHHH
Confidence            69999974 66665433  33 34544 33211   3455666555543110        0011   00     122234


Q ss_pred             hhc--CCceEEEEEeCCCC
Q 039644           63 RRL--SRMKVLIVFDDVTC   79 (192)
Q Consensus        63 ~~l--~~~~~LlVlDdv~~   79 (192)
                      +++  ++++.|+|+||+..
T Consensus       247 Eyfrd~G~~VLlv~DdlTr  265 (497)
T TIGR03324       247 EHFMEQGRDVLIVYDDLTQ  265 (497)
T ss_pred             HHHHhCCCCEEEEEcChhH
Confidence            444  57899999999954

A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 alpha subunit of this apparent second ATP synthase.

>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=86.64  E-value=5.3  Score=28.42  Aligned_cols=107  Identities=12%  Similarity=0.123  Sum_probs=53.5

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHH------HHHHHHhcC-----CCC-cC----chHHHHhh
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQ------KLLSNILKD-----KNV-MP----YIDLNFRR   64 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~------~l~~~~~~~-----~~~-~~----~~~~l~~~   64 (192)
                      +|||||.+.++..... ..+.+++.. .+...  .+...+..      ++++.+.-.     ... ..    ..-.+.+.
T Consensus        36 sGKStLl~~i~G~~~~-~~G~v~~~g-~~~~~--~~~~~~~~~i~~~~q~l~~~gl~~~~~~~~~~LS~G~~qrl~lara  111 (180)
T cd03214          36 AGKSTLLKTLAGLLKP-SSGEILLDG-KDLAS--LSPKELARKIAYVPQALELLGLAHLADRPFNELSGGERQRVLLARA  111 (180)
T ss_pred             CCHHHHHHHHhCCCCC-CCcEEEECC-EECCc--CCHHHHHHHHhHHHHHHHHcCCHhHhcCCcccCCHHHHHHHHHHHH
Confidence            5999999999886533 456666642 11110  11111111      123332211     111 11    22335556


Q ss_pred             cCCceEEEEEeCCCCchh---HHHhhccCCCC-CC-CceEEEEecchhHHhh
Q 039644           65 LSRMKVLIVFDDVTCFSQ---LESLMGSLDWL-TP-VSRIILTTRNKQVLRN  111 (192)
Q Consensus        65 l~~~~~LlVlDdv~~~~~---~~~l~~~~~~~-~~-~~~iivTtR~~~~~~~  111 (192)
                      +-..+-++++|.....-+   .+.+...+... .. +..+|++|........
T Consensus       112 l~~~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tiii~sh~~~~~~~  163 (180)
T cd03214         112 LAQEPPILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVLHDLNLAAR  163 (180)
T ss_pred             HhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHHHHH
Confidence            667889999999974322   22222222211 12 5678888887665433

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.

>PRK06217 hypothetical protein; Validated

Probab=86.56  E-value=4  Score=29.14  Aligned_cols=15  Identities=20%  Similarity=0.496  Sum_probs=13.1

Q ss_pred             CchhHHHHHHHHHhh
Q 039644            1 IGKTAIARAIFDKIS   15 (192)
Q Consensus         1 iGKTtLa~~~~~~~~   15 (192)
                      +||||+|+++...+.
T Consensus        12 sGKSTla~~L~~~l~   26 (183)
T PRK06217         12 SGTTTLGAALAERLD   26 (183)
T ss_pred             CCHHHHHHHHHHHcC
Confidence            699999999999753

>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=86.53  E-value=0.18  Score=38.76  Aligned_cols=16  Identities=25%  Similarity=0.291  Sum_probs=14.0

Q ss_pred             CchhHHHHHHHHHhhC
Q 039644            1 IGKTAIARAIFDKISG   16 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~   16 (192)
                      +||||+|+++...+.+
T Consensus        12 SGKTt~a~~L~~~~~~   27 (270)
T PF08433_consen   12 SGKTTRAKELKKYLEE   27 (270)
T ss_dssp             SSHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHh
Confidence            6999999999997665

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=86.41  E-value=4  Score=36.63  Aligned_cols=66  Identities=12%  Similarity=0.091  Sum_probs=35.4

Q ss_pred             CceEEEEEeCCCCch---------hH-HHhhccCCCCCCCceEEEEecchhHHhhc-------CCCceEecCCCCHHHHH
Q 039644           67 RMKVLIVFDDVTCFS---------QL-ESLMGSLDWLTPVSRIILTTRNKQVLRNW-------GVSKIYEMEALEYHHAL  129 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~---------~~-~~l~~~~~~~~~~~~iivTtR~~~~~~~~-------~~~~~~~l~~l~~~ea~  129 (192)
                      .++.+|++|+++...         +. +-+.+.+.  .+.-++|-+|.........       ...+.+.+...+.++..
T Consensus       270 ~~~~ILfiDEih~l~~~g~~~g~~~~a~lLkp~l~--rg~l~~IgaTt~~ey~~~ie~D~aL~rRf~~I~v~ep~~~e~~  347 (821)
T CHL00095        270 NNNIILVIDEVHTLIGAGAAEGAIDAANILKPALA--RGELQCIGATTLDEYRKHIEKDPALERRFQPVYVGEPSVEETI  347 (821)
T ss_pred             cCCeEEEEecHHHHhcCCCCCCcccHHHHhHHHHh--CCCcEEEEeCCHHHHHHHHhcCHHHHhcceEEecCCCCHHHHH
Confidence            467899999996221         11 22222221  1223455555443322111       23356788888888888


Q ss_pred             HHHHH
Q 039644          130 ELFSQ  134 (192)
Q Consensus       130 ~lf~~  134 (192)
                      .++..
T Consensus       348 aILr~  352 (821)
T CHL00095        348 EILFG  352 (821)
T ss_pred             HHHHH
Confidence            87764

>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=86.30  E-value=0.33  Score=32.88  Aligned_cols=20  Identities=30%  Similarity=0.532  Sum_probs=15.9

Q ss_pred             CchhHHHHHHHHHhhCCCcc
Q 039644            1 IGKTAIARAIFDKISGDFEC   20 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~   20 (192)
                      +|||++|+.++..+...|..
T Consensus        10 ~GKT~la~~lA~~~~~~f~R   29 (131)
T PF07726_consen   10 VGKTTLAKALARSLGLSFKR   29 (131)
T ss_dssp             HHHHHHHHHHHHHTT--EEE
T ss_pred             cHHHHHHHHHHHHcCCceeE
Confidence            59999999999998888865

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.

>PF02572 CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; InterPro: IPR003724 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2

Probab=86.28  E-value=1  Score=32.10  Aligned_cols=51  Identities=18%  Similarity=0.242  Sum_probs=26.7

Q ss_pred             chHHHHhhcCCceE-EEEEeCCCCch-----hHHHhhccCCCCCCCceEEEEecchh
Q 039644           57 YIDLNFRRLSRMKV-LIVFDDVTCFS-----QLESLMGSLDWLTPVSRIILTTRNKQ  107 (192)
Q Consensus        57 ~~~~l~~~l~~~~~-LlVlDdv~~~~-----~~~~l~~~~~~~~~~~~iivTtR~~~  107 (192)
                      ..+..++.+.+..| |+|||.+..--     ..+.+...+........+|+|-|+..
T Consensus        84 ~~~~a~~~i~~~~~dlvILDEi~~a~~~gll~~~~v~~~l~~rp~~~evVlTGR~~~  140 (172)
T PF02572_consen   84 GLEEAKEAISSGEYDLVILDEINYAVDYGLLSEEEVLDLLENRPESLEVVLTGRNAP  140 (172)
T ss_dssp             HHHHHHHHTT-TT-SEEEEETHHHHHHTTSS-HHHHHHHHHTS-TT-EEEEE-SS--
T ss_pred             HHHHHHHHHhCCCCCEEEEcchHHHhHCCCccHHHHHHHHHcCCCCeEEEEECCCCC
Confidence            44555666666655 99999984221     12333333333456788999999865

5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) []. Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type [], EutT-type [] and PduO-type []. Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution. This entry represents the ATP:cob(I)alamin adenosyltransferases CobA (Salmonella typhimurium), CobO (Pseudomonas denitrificans), and ButR (Escherichia coli). There is a high degree of sequence identity between these proteins []. CobA is responsible for attaching the adenosyl moiety from ATP to the cobalt ion of the corrin ring, necessary for the convertion of cobalamin to adenosylcobalamin [, ]. ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid a,c-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process; PDB: 1G64_A 1G5T_A 1G5R_A.

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=86.16  E-value=1.6  Score=36.15  Aligned_cols=72  Identities=18%  Similarity=0.149  Sum_probs=38.1

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHh-------cCCCC--cC----------chHHH
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNIL-------KDKNV--MP----------YIDLN   61 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~-------~~~~~--~~----------~~~~l   61 (192)
                      +|||||+..++..... ..+++++..-+.     ..+.++....+....       .+.++  ..          ..+++
T Consensus       176 sGKTTLL~~Ia~l~~p-d~gvv~liGerg-----rev~e~~~~~l~~~r~rtI~vV~qsd~~~~~r~~~~~~a~~iAEyf  249 (450)
T PRK06002        176 VGKSTLLAMLARADAF-DTVVIALVGERG-----REVREFLEDTLADNLKKAVAVVATSDESPMMRRLAPLTATAIAEYF  249 (450)
T ss_pred             CCHHHHHHHHhCCCCC-CeeeeeecccCC-----ccHHHHhHHHHHHhhCCeEEEEEcCCCCHHHHHHHHHHHHHHHHHH
Confidence            6999999888764432 234555532122     345544443333321       11111  11          33333


Q ss_pred             HhhcCCceEEEEEeCCCCc
Q 039644           62 FRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus        62 ~~~l~~~~~LlVlDdv~~~   80 (192)
                      +.  .+++.|+++||+...
T Consensus       250 rd--~G~~Vll~~DslTr~  266 (450)
T PRK06002        250 RD--RGENVLLIVDSVTRF  266 (450)
T ss_pred             HH--cCCCEEEeccchHHH
Confidence            32  478999999999543

>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=86.14  E-value=2.7  Score=29.56  Aligned_cols=103  Identities=17%  Similarity=0.077  Sum_probs=49.4

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEee---ccccccCCCChHHHHHHHHHHHhc-CCCCcC----chHHHHhhcCCceEEE
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLEN---VREESQRPGGLACLRQKLLSNILK-DKNVMP----YIDLNFRRLSRMKVLI   72 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~---~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~----~~~~l~~~l~~~~~Ll   72 (192)
                      +|||||++.++..... ..+.+++..   ++...+.+. ..  ...+.+.+.. ......    ..-.+.+.+-.++-++
T Consensus        38 sGKSTLl~~l~G~~~~-~~G~i~~~~~~~i~~~~q~~~-~~--~~tv~~nl~~~~~~~LS~G~~~rv~laral~~~p~~l  113 (166)
T cd03223          38 TGKSSLFRALAGLWPW-GSGRIGMPEGEDLLFLPQRPY-LP--LGTLREQLIYPWDDVLSGGEQQRLAFARLLLHKPKFV  113 (166)
T ss_pred             CCHHHHHHHHhcCCCC-CCceEEECCCceEEEECCCCc-cc--cccHHHHhhccCCCCCCHHHHHHHHHHHHHHcCCCEE
Confidence            5999999999885432 234333321   111122211 10  0122222211 111111    3333555666788899


Q ss_pred             EEeCCCCchh---HHHhhccCCCCCCCceEEEEecchhHH
Q 039644           73 VFDDVTCFSQ---LESLMGSLDWLTPVSRIILTTRNKQVL  109 (192)
Q Consensus        73 VlDdv~~~~~---~~~l~~~~~~~~~~~~iivTtR~~~~~  109 (192)
                      +||...+.-+   ...+...+...  +..+|++|.+....
T Consensus       114 llDEPt~~LD~~~~~~l~~~l~~~--~~tiiivsh~~~~~  151 (166)
T cd03223         114 FLDEATSALDEESEDRLYQLLKEL--GITVISVGHRPSLW  151 (166)
T ss_pred             EEECCccccCHHHHHHHHHHHHHh--CCEEEEEeCChhHH
Confidence            9999864322   22222222222  35588888776544

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

>CHL00060 atpB ATP synthase CF1 beta subunit

Probab=85.84  E-value=3.2  Score=34.73  Aligned_cols=76  Identities=17%  Similarity=0.152  Sum_probs=42.7

Q ss_pred             CchhHHHHHHHHHhhCCC-cceEEEeeccccccCCCChHHHHHHHHHHHhcCC--------------CC-c---C-----
Q 039644            1 IGKTAIARAIFDKISGDF-ECSCFLENVREESQRPGGLACLRQKLLSNILKDK--------------NV-M---P-----   56 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F-~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~--------------~~-~---~-----   56 (192)
                      +|||+|+.+++..+.... +.+++.- +++-.   ....+++..++..-....              .+ .   .     
T Consensus       172 vGKs~L~~~~~~~~~~~~~dv~V~~l-IGERg---rEv~efi~~~~~~~~~~~~~~~~~rsvvv~atsd~p~~~R~~a~~  247 (494)
T CHL00060        172 VGKTVLIMELINNIAKAHGGVSVFGG-VGERT---REGNDLYMEMKESGVINEQNIAESKVALVYGQMNEPPGARMRVGL  247 (494)
T ss_pred             CChhHHHHHHHHHHHHhcCCeEEEEE-eccCc---hHHHHHHHHHHhcCccccCcccccceEEEEECCCCCHHHHHHHHH
Confidence            699999999988743222 4555554 44321   346667766655211110              00 0   0     


Q ss_pred             chHHHHhhcC--C-ceEEEEEeCCCCc
Q 039644           57 YIDLNFRRLS--R-MKVLIVFDDVTCF   80 (192)
Q Consensus        57 ~~~~l~~~l~--~-~~~LlVlDdv~~~   80 (192)
                      ..-.+.++++  + ++.||++||+...
T Consensus       248 ~A~tiAEyfrd~g~~~VLll~DslTR~  274 (494)
T CHL00060        248 TALTMAEYFRDVNKQDVLLFIDNIFRF  274 (494)
T ss_pred             HHHHHHHHHHHcCCCCEEEEcccchHH
Confidence            2333556663  3 4999999999543

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=85.67  E-value=9.7  Score=28.93  Aligned_cols=25  Identities=16%  Similarity=0.046  Sum_probs=19.0

Q ss_pred             CchhHHHHHHHHHhhCC-CcceEEEe
Q 039644            1 IGKTAIARAIFDKISGD-FECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~-F~~~~wv~   25 (192)
                      +|||+++.+++...... -..++|++
T Consensus        41 ~GKT~l~~~~~~~~~~~~g~~vl~iS   66 (271)
T cd01122          41 VGKTTFLREYALDLITQHGVRVGTIS   66 (271)
T ss_pred             CCHHHHHHHHHHHHHHhcCceEEEEE
Confidence            69999999998875333 45677886

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

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

Probab=85.65  E-value=0.84  Score=34.95  Aligned_cols=77  Identities=10%  Similarity=0.090  Sum_probs=43.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-cCchHHHHhhcCCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV-MPYIDLNFRRLSRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~~~~~l~~~l~~~~~LlVlDdv~~   79 (192)
                      +||||++..+...+...-..++-+.+..+..     +..     ..++.-.... ......++..++..+=.|+++.+.+
T Consensus        91 SGKTT~l~all~~i~~~~~~iitiEdp~E~~-----~~~-----~~q~~v~~~~~~~~~~~l~~~lR~~PD~i~vgEiR~  160 (264)
T cd01129          91 SGKTTTLYSALSELNTPEKNIITVEDPVEYQ-----IPG-----INQVQVNEKAGLTFARGLRAILRQDPDIIMVGEIRD  160 (264)
T ss_pred             CcHHHHHHHHHhhhCCCCCeEEEECCCceec-----CCC-----ceEEEeCCcCCcCHHHHHHHHhccCCCEEEeccCCC
Confidence            5999999999887644222334443222211     000     0111111111 2255667777888888999999998


Q ss_pred             chhHHHhh
Q 039644           80 FSQLESLM   87 (192)
Q Consensus        80 ~~~~~~l~   87 (192)
                      .+....+.
T Consensus       161 ~e~a~~~~  168 (264)
T cd01129         161 AETAEIAV  168 (264)
T ss_pred             HHHHHHHH
Confidence            87655443

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.

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

Probab=85.40  E-value=4.5  Score=34.95  Aligned_cols=19  Identities=32%  Similarity=0.469  Sum_probs=16.5

Q ss_pred             CchhHHHHHHHHHhhCCCc
Q 039644            1 IGKTAIARAIFDKISGDFE   19 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~   19 (192)
                      +|||++|+.+++.....|-
T Consensus       479 C~KT~lAkalAne~~~nFl  497 (693)
T KOG0730|consen  479 CGKTLLAKALANEAGMNFL  497 (693)
T ss_pred             cchHHHHHHHhhhhcCCee
Confidence            6999999999998877764

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=85.34  E-value=3  Score=32.64  Aligned_cols=26  Identities=15%  Similarity=0.197  Sum_probs=18.7

Q ss_pred             CchhHHHHHHHHHhhCC------CcceEEEee
Q 039644            1 IGKTAIARAIFDKISGD------FECSCFLEN   26 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~------F~~~~wv~~   26 (192)
                      +|||+|+.+++......      =..++|++.
T Consensus       106 ~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~t  137 (310)
T TIGR02236       106 SGKTQICHQLAVNVQLPEEKGGLGGKAVYIDT  137 (310)
T ss_pred             CCHHHHHHHHHHHhcCCcccCCCcceEEEEEC
Confidence            69999999998864321      126888873

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.

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=85.22  E-value=1.2  Score=30.64  Aligned_cols=25  Identities=16%  Similarity=0.434  Sum_probs=17.9

Q ss_pred             CchhHHHHHHHHHhh-CCCcceEEEe
Q 039644            1 IGKTAIARAIFDKIS-GDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~-~~F~~~~wv~   25 (192)
                      +|||||++.+++.+. ..+...+...
T Consensus        11 sGKTTl~~~Li~~l~~~g~~v~~ik~   36 (140)
T PF03205_consen   11 SGKTTLIRKLINELKRRGYRVAVIKH   36 (140)
T ss_dssp             SSHHHHHHHHHHHHHHTT--EEEEEE
T ss_pred             CCHHHHHHHHHHHHhHcCCceEEEEE
Confidence            699999999999865 5555555554

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=85.15  E-value=1.5  Score=30.79  Aligned_cols=103  Identities=17%  Similarity=0.147  Sum_probs=51.0

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhc--CCCC-cCchHHHHhhcCCceEEEEEeCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILK--DKNV-MPYIDLNFRRLSRMKVLIVFDDV   77 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~--~~~~-~~~~~~l~~~l~~~~~LlVlDdv   77 (192)
                      +|||||.+.++.... ...+.+++... +...  ....+...   ..+.-  +-+. ....-.+.+.+-..+-++++|+.
T Consensus        37 sGKSTLl~~i~G~~~-~~~G~v~~~g~-~~~~--~~~~~~~~---~~i~~~~qLS~G~~qrl~laral~~~p~illlDEP  109 (163)
T cd03216          37 AGKSTLMKILSGLYK-PDSGEILVDGK-EVSF--ASPRDARR---AGIAMVYQLSVGERQMVEIARALARNARLLILDEP  109 (163)
T ss_pred             CCHHHHHHHHhCCCC-CCCeEEEECCE-ECCc--CCHHHHHh---cCeEEEEecCHHHHHHHHHHHHHhcCCCEEEEECC
Confidence            599999999988543 24566666521 1110  11111110   01100  0010 11223355556677889999999


Q ss_pred             CCchh---HHHhhccCCCC-CCCceEEEEecchhHHh
Q 039644           78 TCFSQ---LESLMGSLDWL-TPVSRIILTTRNKQVLR  110 (192)
Q Consensus        78 ~~~~~---~~~l~~~~~~~-~~~~~iivTtR~~~~~~  110 (192)
                      .+.-+   .+.+...+... ..+..||++|.+.....
T Consensus       110 ~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~~~~  146 (163)
T cd03216         110 TAALTPAEVERLFKVIRRLRAQGVAVIFISHRLDEVF  146 (163)
T ss_pred             CcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHHHH
Confidence            75322   22222222211 23556888888766443

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.

>PTZ00035 Rad51 protein; Provisional

Probab=85.05  E-value=4  Score=32.47  Aligned_cols=26  Identities=12%  Similarity=0.144  Sum_probs=17.0

Q ss_pred             CchhHHHHHHHHHhhC------CCcceEEEee
Q 039644            1 IGKTAIARAIFDKISG------DFECSCFLEN   26 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~------~F~~~~wv~~   26 (192)
                      +|||+|+..++-...-      .=..++|++.
T Consensus       129 sGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdt  160 (337)
T PTZ00035        129 TGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDT  160 (337)
T ss_pred             CchhHHHHHHHHHhccccccCCCCceEEEEEc
Confidence            6999999998864331      1124568873

>PRK05922 type III secretion system ATPase; Validated

Probab=84.99  E-value=2.2  Score=35.10  Aligned_cols=15  Identities=20%  Similarity=0.268  Sum_probs=12.4

Q ss_pred             CchhHHHHHHHHHhh
Q 039644            1 IGKTAIARAIFDKIS   15 (192)
Q Consensus         1 iGKTtLa~~~~~~~~   15 (192)
                      +|||||.+.++....
T Consensus       168 ~GKSTLL~~Ia~~~~  182 (434)
T PRK05922        168 SGKSSLLSTIAKGSK  182 (434)
T ss_pred             CChHHHHHHHhccCC
Confidence            699999999987653

>PRK08149 ATP synthase SpaL; Validated

Probab=84.96  E-value=1.8  Score=35.53  Aligned_cols=74  Identities=11%  Similarity=0.163  Sum_probs=38.6

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhc--------CCCC---cC-----chHHHHhh
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILK--------DKNV---MP-----YIDLNFRR   64 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~--------~~~~---~~-----~~~~l~~~   64 (192)
                      +|||||...++.....  +.++... +.   .....+.++....+.....        ..+.   ..     ..-.+.++
T Consensus       162 ~GKTTLl~~i~~~~~~--dv~v~g~-Ig---~rg~ev~e~~~~~l~~~~~~~~~vV~~~sd~p~~~r~~a~~~a~tiAE~  235 (428)
T PRK08149        162 CGKTSLMNMLIEHSEA--DVFVIGL-IG---ERGREVTEFVESLRASSRREKCVLVYATSDFSSVDRCNAALVATTVAEY  235 (428)
T ss_pred             CChhHHHHHHhcCCCC--CeEEEEE-Ee---eCCccHHHHHHHHhhcccccceEEEEECCCCCHHHHHhHHHHHHHHHHH
Confidence            6999999988874332  1222211 11   1114566666666553211        1111   00     12223333


Q ss_pred             c--CCceEEEEEeCCCCc
Q 039644           65 L--SRMKVLIVFDDVTCF   80 (192)
Q Consensus        65 l--~~~~~LlVlDdv~~~   80 (192)
                      +  .+++.|+++||+...
T Consensus       236 fr~~G~~Vll~~DslTr~  253 (428)
T PRK08149        236 FRDQGKRVVLFIDSMTRY  253 (428)
T ss_pred             HHHcCCCEEEEccchHHH
Confidence            3  478999999999543

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=84.96  E-value=17  Score=28.45  Aligned_cols=118  Identities=11%  Similarity=0.085  Sum_probs=70.4

Q ss_pred             ceE-EEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchhH--HhhcCCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           68 MKV-LIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQV--LRNWGVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        68 ~~~-LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~~--~~~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      ++| ++|+-.+++..  .-..++.....+.+.+|+|+.....+.  ...-+..-.+++...+.+|....+.+..-.....
T Consensus       126 r~fKvvvi~ead~LT~dAQ~aLRRTMEkYs~~~RlIl~cns~SriIepIrSRCl~iRvpaps~eeI~~vl~~v~~kE~l~  205 (351)
T KOG2035|consen  126 RPFKVVVINEADELTRDAQHALRRTMEKYSSNCRLILVCNSTSRIIEPIRSRCLFIRVPAPSDEEITSVLSKVLKKEGLQ  205 (351)
T ss_pred             cceEEEEEechHhhhHHHHHHHHHHHHHHhcCceEEEEecCcccchhHHhhheeEEeCCCCCHHHHHHHHHHHHHHhccc
Confidence            455 55666665432  233444444445677888886544321  1111233467888999999999988876433322


Q ss_pred             CccHHHHHHHHHHHhCCCchHHHHHHHHhcc-------C--C--HHHHHHHHHHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLALKVLSCFLHK-------R--E--KEVWESAIDKLQ  187 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai~~~~~~l~~-------~--~--~~~w~~~l~~l~  187 (192)
                      -  ..+.+.+|+++++|.-.-...+....+-       +  .  ..+|+-++.++-
T Consensus       206 l--p~~~l~rIa~kS~~nLRrAllmlE~~~~~n~~~~a~~~~i~~~dWe~~i~e~a  259 (351)
T KOG2035|consen  206 L--PKELLKRIAEKSNRNLRRALLMLEAVRVNNEPFTANSQVIPKPDWEIYIQEIA  259 (351)
T ss_pred             C--cHHHHHHHHHHhcccHHHHHHHHHHHHhccccccccCCCCCCccHHHHHHHHH
Confidence            2  3678899999999875544444333321       1  1  578998887654

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=84.94  E-value=3.5  Score=34.04  Aligned_cols=74  Identities=12%  Similarity=0.181  Sum_probs=38.5

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhc--------CCCC--cC------chHHHHhh
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILK--------DKNV--MP------YIDLNFRR   64 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~--------~~~~--~~------~~~~l~~~   64 (192)
                      +|||||++.++.....  +.++.. .+++-.   ..+.++...++..-.-        ..++  ..      ..-.+.++
T Consensus       173 ~GKSTLL~~I~~~~~~--dv~Vi~-lIGER~---rEv~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~a~~~A~tiAEy  246 (444)
T PRK08972        173 VGKSVLLGMMTRGTTA--DVIVVG-LVGERG---REVKEFIEEILGEEGRARSVVVAAPADTSPLMRLKGCETATTIAEY  246 (444)
T ss_pred             CChhHHHHHhccCCCC--CEEEEE-EEcCCh---HHHHHHHHHhhccCCcccEEEEEECCCCCHHHHHHHHHHHHHHHHH
Confidence            5999999999875433  334443 233311   3455555554333110        0011  00      12223333


Q ss_pred             c--CCceEEEEEeCCCCc
Q 039644           65 L--SRMKVLIVFDDVTCF   80 (192)
Q Consensus        65 l--~~~~~LlVlDdv~~~   80 (192)
                      +  .+++.|+++||+...
T Consensus       247 frd~G~~VLl~~DslTR~  264 (444)
T PRK08972        247 FRDQGLNVLLLMDSLTRY  264 (444)
T ss_pred             HHHcCCCEEEEEcChHHH
Confidence            3  578999999999543

>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI

Probab=84.94  E-value=1.7  Score=35.56  Aligned_cols=15  Identities=33%  Similarity=0.583  Sum_probs=12.4

Q ss_pred             CCceEEEEEeCCCCc
Q 039644           66 SRMKVLIVFDDVTCF   80 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~   80 (192)
                      .+++.|+++||+...
T Consensus       225 ~G~~Vll~~Dsltr~  239 (411)
T TIGR03496       225 QGKDVLLLMDSLTRF  239 (411)
T ss_pred             CCCCEEEEEeChHHH
Confidence            478999999999543

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=84.82  E-value=7.1  Score=26.92  Aligned_cols=15  Identities=47%  Similarity=0.632  Sum_probs=13.3

Q ss_pred             CchhHHHHHHHHHhh
Q 039644            1 IGKTAIARAIFDKIS   15 (192)
Q Consensus         1 iGKTtLa~~~~~~~~   15 (192)
                      +||||||+.+...+.
T Consensus        10 sGKSTla~~L~~~l~   24 (149)
T cd02027          10 SGKSTIARALEEKLF   24 (149)
T ss_pred             CCHHHHHHHHHHHHH
Confidence            699999999999764

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>KOG2383 consensus Predicted ATPase [General function prediction only]

Probab=84.79  E-value=1.3  Score=35.94  Aligned_cols=49  Identities=16%  Similarity=0.272  Sum_probs=31.2

Q ss_pred             CchHHHHhhcCCceEEEEEeCCCCchh-----HHHhhccCCCCCCCceEEEEecchh
Q 039644           56 PYIDLNFRRLSRMKVLIVFDDVTCFSQ-----LESLMGSLDWLTPVSRIILTTRNKQ  107 (192)
Q Consensus        56 ~~~~~l~~~l~~~~~LlVlDdv~~~~~-----~~~l~~~~~~~~~~~~iivTtR~~~  107 (192)
                      +.+..+.......-+||+||.+.-.+.     +..+...+.  .+|. |+|.|.++.
T Consensus       181 Dpl~~vA~eIa~ea~lLCFDEfQVTDVADAmiL~rLf~~Lf--~~Gv-VlvATSNR~  234 (467)
T KOG2383|consen  181 DPLPVVADEIAEEAILLCFDEFQVTDVADAMILKRLFEHLF--KNGV-VLVATSNRA  234 (467)
T ss_pred             CccHHHHHHHhhhceeeeechhhhhhHHHHHHHHHHHHHHH--hCCe-EEEEeCCCC
Confidence            366677777778899999999974432     455555543  3355 555555543

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=84.53  E-value=12  Score=27.49  Aligned_cols=53  Identities=9%  Similarity=0.056  Sum_probs=34.8

Q ss_pred             HHHHhhcCCceEEEEEeCCC----CchhHHHhhccCCC-CCCCceEEEEecchhHHhhc
Q 039644           59 DLNFRRLSRMKVLIVFDDVT----CFSQLESLMGSLDW-LTPVSRIILTTRNKQVLRNW  112 (192)
Q Consensus        59 ~~l~~~l~~~~~LlVlDdv~----~~~~~~~l~~~~~~-~~~~~~iivTtR~~~~~~~~  112 (192)
                      -.+.+.+-+++-+|+-|.-.    ....|+-+. .+.. +..|+.|++.|.+..+...+
T Consensus       146 vaIARAiV~~P~vLlADEPTGNLDp~~s~~im~-lfeeinr~GtTVl~ATHd~~lv~~~  203 (223)
T COG2884         146 VAIARAIVNQPAVLLADEPTGNLDPDLSWEIMR-LFEEINRLGTTVLMATHDLELVNRM  203 (223)
T ss_pred             HHHHHHHccCCCeEeecCCCCCCChHHHHHHHH-HHHHHhhcCcEEEEEeccHHHHHhc
Confidence            34666667889999998653    333343221 1111 34788999999999888776

>PRK11823 DNA repair protein RadA; Provisional

Probab=84.40  E-value=3.7  Score=34.05  Aligned_cols=70  Identities=9%  Similarity=0.193  Sum_probs=38.4

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCc-----CchHHHHhhcC-CceEEEEE
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVM-----PYIDLNFRRLS-RMKVLIVF   74 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~-----~~~~~l~~~l~-~~~~LlVl   74 (192)
                      +|||||+.+++.....+-..++|++. .      .....+... .+.+..+.+..     .....+...+. .++-++|+
T Consensus        91 ~GKTtL~lq~a~~~a~~g~~vlYvs~-E------es~~qi~~r-a~rlg~~~~~l~~~~e~~l~~i~~~i~~~~~~lVVI  162 (446)
T PRK11823         91 IGKSTLLLQVAARLAAAGGKVLYVSG-E------ESASQIKLR-AERLGLPSDNLYLLAETNLEAILATIEEEKPDLVVI  162 (446)
T ss_pred             CCHHHHHHHHHHHHHhcCCeEEEEEc-c------ccHHHHHHH-HHHcCCChhcEEEeCCCCHHHHHHHHHhhCCCEEEE
Confidence            69999999999976543345678762 1      123333222 22332211110     13344444443 35668999


Q ss_pred             eCCC
Q 039644           75 DDVT   78 (192)
Q Consensus        75 Ddv~   78 (192)
                      |.+.
T Consensus       163 DSIq  166 (446)
T PRK11823        163 DSIQ  166 (446)
T ss_pred             echh
Confidence            9985

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

Probab=84.35  E-value=0.8  Score=33.15  Aligned_cols=17  Identities=24%  Similarity=0.393  Sum_probs=14.4

Q ss_pred             CchhHHHHHHHHHhhCC
Q 039644            1 IGKTAIARAIFDKISGD   17 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~   17 (192)
                      +||||+|+.+...+...
T Consensus        10 SGKTTla~~L~~~L~~~   26 (194)
T PF00485_consen   10 SGKTTLAKRLAQILNKR   26 (194)
T ss_dssp             SSHHHHHHHHHHHHTTC
T ss_pred             CCHHHHHHHHHHHhCcc
Confidence            69999999999987643

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 ....

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

Probab=84.18  E-value=4.9  Score=31.95  Aligned_cols=25  Identities=24%  Similarity=0.426  Sum_probs=18.1

Q ss_pred             CchhHHHHHHHHH----hhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDK----ISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~----~~~~F~~~~wv~   25 (192)
                      .|||+|.+.++++    ...+|....-+.
T Consensus       188 TGKTSLCKaLaQkLSIR~~~~y~~~~liE  216 (423)
T KOG0744|consen  188 TGKTSLCKALAQKLSIRTNDRYYKGQLIE  216 (423)
T ss_pred             CChhHHHHHHHHhheeeecCccccceEEE
Confidence            4999999999995    345565555554

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=83.95  E-value=2.4  Score=33.60  Aligned_cols=74  Identities=18%  Similarity=0.171  Sum_probs=37.9

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHh-------cCCCC---cC------chHHHHhh
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNIL-------KDKNV---MP------YIDLNFRR   64 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~-------~~~~~---~~------~~~~l~~~   64 (192)
                      +|||||.+.++......  ..+... ++.   ....+.++....+..-.       ....+   ..      ..-.+.++
T Consensus        80 ~GKTtLl~~Ia~~~~~~--~~vi~~-iGe---r~~ev~~~~~~~~~~~~l~rtvvv~~t~d~~~~~r~~~~~~a~~~AEy  153 (326)
T cd01136          80 VGKSTLLGMIARGTTAD--VNVIAL-IGE---RGREVREFIEKDLGEEGLKRSVVVVATSDESPLLRVKAAYTATAIAEY  153 (326)
T ss_pred             CChHHHHHHHhCCCCCC--EEEEEE-Eec---CCccHHHHHHHHHhcCccceEEEEEcCCCCCHHHHHHHHHHHHHHHHH
Confidence            59999999988865432  222222 211   11455565555544311       01111   11      12223333


Q ss_pred             c--CCceEEEEEeCCCCc
Q 039644           65 L--SRMKVLIVFDDVTCF   80 (192)
Q Consensus        65 l--~~~~~LlVlDdv~~~   80 (192)
                      +  .+++.|+++||+...
T Consensus       154 fr~~g~~Vll~~Dsltr~  171 (326)
T cd01136         154 FRDQGKDVLLLMDSLTRF  171 (326)
T ss_pred             HHHcCCCeEEEeccchHH
Confidence            3  478999999998543

This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=83.93  E-value=2.9  Score=32.07  Aligned_cols=109  Identities=16%  Similarity=0.102  Sum_probs=59.8

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccC-CCChHHHHHHHHHHHhcCCCC-------cC----chHHHHhhcCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQR-PGGLACLRQKLLSNILKDKNV-------MP----YIDLNFRRLSRM   68 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~-------~~----~~~~l~~~l~~~   68 (192)
                      +||||+++.+..-.+.- .+.+++.+ .+...- .....+...+++..++...+.       .+    -.-.+.+.+.-+
T Consensus        50 ~GKSTlgr~i~~L~~pt-~G~i~f~g-~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGGQrQRi~IARALal~  127 (268)
T COG4608          50 CGKSTLGRLILGLEEPT-SGEILFEG-KDITKLSKEERRERVLELLEKVGLPEEFLYRYPHELSGGQRQRIGIARALALN  127 (268)
T ss_pred             CCHHHHHHHHHcCcCCC-CceEEEcC-cchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCcccCchhhhhHHHHHHHhhC
Confidence            69999999999855433 34555542 111000 023445556666666533211       11    222356667788


Q ss_pred             eEEEEEeCCCCchh------HHHhhccCCCCCCCceEEEEecchhHHhhc
Q 039644           69 KVLIVFDDVTCFSQ------LESLMGSLDWLTPVSRIILTTRNKQVLRNW  112 (192)
Q Consensus        69 ~~LlVlDdv~~~~~------~~~l~~~~~~~~~~~~iivTtR~~~~~~~~  112 (192)
                      +-++|.|...+.-+      .-.+...+.. ..|-..+..|.+-.+...+
T Consensus       128 P~liV~DEpvSaLDvSiqaqIlnLL~dlq~-~~~lt~lFIsHDL~vv~~i  176 (268)
T COG4608         128 PKLIVADEPVSALDVSVQAQILNLLKDLQE-ELGLTYLFISHDLSVVRYI  176 (268)
T ss_pred             CcEEEecCchhhcchhHHHHHHHHHHHHHH-HhCCeEEEEEEEHHhhhhh
Confidence            99999999875432      1122222221 2344577777777766665

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=83.69  E-value=5  Score=33.25  Aligned_cols=76  Identities=16%  Similarity=0.150  Sum_probs=42.9

Q ss_pred             CchhHHHHHHHHHhh-CCCcceEEEeeccccccCCCChHHHHHHHHHHHhc--------CCCC--cC------chHHHHh
Q 039644            1 IGKTAIARAIFDKIS-GDFECSCFLENVREESQRPGGLACLRQKLLSNILK--------DKNV--MP------YIDLNFR   63 (192)
Q Consensus         1 iGKTtLa~~~~~~~~-~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~--------~~~~--~~------~~~~l~~   63 (192)
                      +|||+|+.+++.... .+-+.+++.- +++-   .....++...+...-.-        ..++  ..      ..-.+.+
T Consensus       149 ~GKt~l~~~~~~~~~~~~~~v~V~~~-iGeR---~rEv~e~~~~~~~~~~l~rtvvv~~ts~~~~~~r~~~~~~a~tiAE  224 (449)
T TIGR03305       149 VGKTVLLTEMIHNMVGQHQGVSIFCG-IGER---CREGEELYREMKEAGVLDNTVMVFGQMNEPPGARFRVGHTALTMAE  224 (449)
T ss_pred             CChhHHHHHHHHHHHhcCCCEEEEEE-eccC---cHHHHHHHHHHhhccccceEEEEEeCCCCCHHHHHHHHHHHHHHHH
Confidence            699999999988654 3235566654 4331   13455666665443110        0011  00      2333445


Q ss_pred             hc---CCceEEEEEeCCCCc
Q 039644           64 RL---SRMKVLIVFDDVTCF   80 (192)
Q Consensus        64 ~l---~~~~~LlVlDdv~~~   80 (192)
                      ++   .+++.|+++||+...
T Consensus       225 yfrd~~G~~VLl~~DslTR~  244 (449)
T TIGR03305       225 YFRDDEKQDVLLLIDNIFRF  244 (449)
T ss_pred             HHHHhcCCceEEEecChHHH
Confidence            54   358999999999643

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.

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=83.63  E-value=1.6  Score=32.28  Aligned_cols=47  Identities=15%  Similarity=0.193  Sum_probs=28.5

Q ss_pred             CCceEEEEEeCCCCchh-------HHHhhccCCCC-CCCceEEEEecchhHHhhc
Q 039644           66 SRMKVLIVFDDVTCFSQ-------LESLMGSLDWL-TPVSRIILTTRNKQVLRNW  112 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~~~-------~~~l~~~~~~~-~~~~~iivTtR~~~~~~~~  112 (192)
                      ...+.|++||......+       ...+...+... ..+..+|++|.........
T Consensus       106 ~~~~slvllDE~~~gtd~~~~~~~~~ail~~l~~~~~~~~~vli~TH~~~l~~~~  160 (213)
T cd03281         106 ATRRSLVLIDEFGKGTDTEDGAGLLIATIEHLLKRGPECPRVIVSTHFHELFNRS  160 (213)
T ss_pred             CCCCcEEEeccccCCCCHHHHHHHHHHHHHHHHhcCCCCcEEEEEcChHHHHHhh
Confidence            36789999999975432       11222233222 2234799999987776654

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

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=83.49  E-value=5.8  Score=28.80  Aligned_cols=32  Identities=19%  Similarity=0.309  Sum_probs=20.0

Q ss_pred             EEEEEeCCCCc--hhHHHhhccCCCCCCCceEEEEe
Q 039644           70 VLIVFDDVTCF--SQLESLMGSLDWLTPVSRIILTT  103 (192)
Q Consensus        70 ~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~iivTt  103 (192)
                      -++|+|.+.-.  ..+..+....+.  .++++|+.-
T Consensus        95 ~vliVDEasmv~~~~~~~ll~~~~~--~~~klilvG  128 (196)
T PF13604_consen   95 DVLIVDEASMVDSRQLARLLRLAKK--SGAKLILVG  128 (196)
T ss_dssp             SEEEESSGGG-BHHHHHHHHHHS-T---T-EEEEEE
T ss_pred             cEEEEecccccCHHHHHHHHHHHHh--cCCEEEEEC
Confidence            49999999744  457777666554  466777654

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=83.46  E-value=4.1  Score=32.14  Aligned_cols=26  Identities=15%  Similarity=0.226  Sum_probs=17.2

Q ss_pred             CchhHHHHHHHHHhh--CCC----cceEEEee
Q 039644            1 IGKTAIARAIFDKIS--GDF----ECSCFLEN   26 (192)
Q Consensus         1 iGKTtLa~~~~~~~~--~~F----~~~~wv~~   26 (192)
                      +|||+|+..++..+.  ...    ..++|++.
T Consensus       107 ~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdt  138 (316)
T TIGR02239       107 TGKTQLCHTLAVTCQLPIDQGGGEGKALYIDT  138 (316)
T ss_pred             CCcCHHHHHHHHHHhhhhhcCCCCceEEEEEC
Confidence            699999999986321  111    24588873

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).

>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A

Probab=83.41  E-value=4.6  Score=32.38  Aligned_cols=39  Identities=13%  Similarity=0.214  Sum_probs=23.4

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHH
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLL   45 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~   45 (192)
                      +|||+|+.++++....  +.++++- +++-   ...+.+++.++-
T Consensus       168 ~GKT~L~~~Iak~~~~--dvvVyv~-iGER---g~Ev~e~l~ef~  206 (369)
T cd01134         168 CGKTVIQQSLSKYSNS--DIVIYVG-CGER---GNEMTEVLEEFP  206 (369)
T ss_pred             CChHHHHHHHHhCCCC--CEEEEEE-eCCC---hHHHHHHHHHHH
Confidence            6999999999986433  3556554 3221   134555555543

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.

>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=83.38  E-value=9.8  Score=27.71  Aligned_cols=25  Identities=12%  Similarity=0.178  Sum_probs=16.7

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +||||.+-+++.+.+.+-..+..++
T Consensus        12 vGKTTt~aKLAa~~~~~~~~v~lis   36 (196)
T PF00448_consen   12 VGKTTTIAKLAARLKLKGKKVALIS   36 (196)
T ss_dssp             SSHHHHHHHHHHHHHHTT--EEEEE
T ss_pred             CchHhHHHHHHHHHhhccccceeec
Confidence            6999999999987654433444444

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 ....

>PF06144 DNA_pol3_delta: DNA polymerase III, delta subunit; InterPro: IPR010372 DNA polymerase III, delta subunit (2

Probab=83.29  E-value=13  Score=25.93  Aligned_cols=96  Identities=10%  Similarity=0.051  Sum_probs=49.7

Q ss_pred             ceEEEEEeCC------CCchhHHHhhccCCCCCCCceEEEEec-chh----HHhhc-CCCceEecCCCCHHHHHHHHHHh
Q 039644           68 MKVLIVFDDV------TCFSQLESLMGSLDWLTPVSRIILTTR-NKQ----VLRNW-GVSKIYEMEALEYHHALELFSQH  135 (192)
Q Consensus        68 ~~~LlVlDdv------~~~~~~~~l~~~~~~~~~~~~iivTtR-~~~----~~~~~-~~~~~~~l~~l~~~ea~~lf~~~  135 (192)
                      .+-++|+.+.      .....++.+...+.+..+++.+|+.+. ...    ..... .....+...++...+....+...
T Consensus        57 ~~klvii~~~~~l~~~~~~~~~~~l~~~l~~~~~~~~lii~~~~~~~~~~k~~k~l~~~~~~~~~~~~~~~~~~~~i~~~  136 (172)
T PF06144_consen   57 DKKLVIIKNAPFLKDKLKKKEIKALIEYLSNPPPDCILIIFSEEKLDKRKKLYKALKKQAIVIECKKPKEQELPRWIKER  136 (172)
T ss_dssp             SEEEEEEE-----TT-S-TTHHHHHHHHTTT--SSEEEEEEES-S--HHHHHHHHHTTTEEEEEE----TTTHHHHHHHH
T ss_pred             CCeEEEEecCccccccccHHHHHHHHHHHhCCCCCEEEEEEeCCchhhhhhHHHHHhcccceEEecCCCHHHHHHHHHHH
Confidence            4567777776      234568888888877677888888877 222    11112 23445667777777776666655


Q ss_pred             hcCCCCCCccHHHHHHHHHHHhCCCchHHH
Q 039644          136 AFKRNHPDVGYEKLSSNVTKYAQGIPLALK  165 (192)
Q Consensus       136 ~~~~~~~~~~~~~~~~~i~~~~~g~Plai~  165 (192)
                      +-...  -.-..+....+++.+++.+.++.
T Consensus       137 ~~~~g--~~i~~~a~~~L~~~~~~d~~~l~  164 (172)
T PF06144_consen  137 AKKNG--LKIDPDAAQYLIERVGNDLSLLQ  164 (172)
T ss_dssp             HHHTT---EE-HHHHHHHHHHHTT-HHHHH
T ss_pred             HHHcC--CCCCHHHHHHHHHHhChHHHHHH
Confidence            53222  12344556667777777665543

7.7.7 from EC) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalysed reaction []. The delta subunit is also known as HolA.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0009360 DNA polymerase III complex; PDB: 3GLG_F 1XXH_A 1JQL_B 3GLF_F 1JQJ_C 3GLI_F.

>PTZ00301 uridine kinase; Provisional

Probab=83.28  E-value=0.82  Score=33.75  Aligned_cols=18  Identities=17%  Similarity=0.396  Sum_probs=14.2

Q ss_pred             CchhHHHHHHHHHhhCCC
Q 039644            1 IGKTAIARAIFDKISGDF   18 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F   18 (192)
                      +||||||..+.+++...+
T Consensus        14 SGKTTla~~l~~~l~~~~   31 (210)
T PTZ00301         14 SGKSSLSTNIVSELMAHC   31 (210)
T ss_pred             CCHHHHHHHHHHHHHhhc
Confidence            699999999988764433

>TIGR00416 sms DNA repair protein RadA

Probab=83.14  E-value=3.8  Score=34.03  Aligned_cols=25  Identities=12%  Similarity=0.220  Sum_probs=19.3

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +|||||+.+++.....+-..++|++
T Consensus       105 sGKTTL~lq~a~~~a~~g~kvlYvs  129 (454)
T TIGR00416       105 IGKSTLLLQVACQLAKNQMKVLYVS  129 (454)
T ss_pred             CCHHHHHHHHHHHHHhcCCcEEEEE
Confidence            6999999999887654434577886

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)).

>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=83.09  E-value=0.98  Score=26.76  Aligned_cols=14  Identities=21%  Similarity=0.605  Sum_probs=12.7

Q ss_pred             CchhHHHHHHHHHh
Q 039644            1 IGKTAIARAIFDKI   14 (192)
Q Consensus         1 iGKTtLa~~~~~~~   14 (192)
                      +||||+++.+.+.+
T Consensus        10 sGKst~~~~l~~~l   23 (69)
T cd02019          10 SGKSTVAKKLAEQL   23 (69)
T ss_pred             CCHHHHHHHHHHHh
Confidence            69999999999985

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.

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

Probab=82.97  E-value=1.7  Score=35.08  Aligned_cols=18  Identities=22%  Similarity=0.298  Sum_probs=15.3

Q ss_pred             CchhHHHHHHHHHhhCCC
Q 039644            1 IGKTAIARAIFDKISGDF   18 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F   18 (192)
                      +|||.+|+.++.+....|
T Consensus       159 cGKTllAraiA~elg~~~  176 (413)
T PLN00020        159 QGKSFQCELVFKKMGIEP  176 (413)
T ss_pred             CCHHHHHHHHHHHcCCCe
Confidence            699999999999876553

>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]

Probab=82.88  E-value=2.8  Score=30.90  Aligned_cols=25  Identities=16%  Similarity=0.109  Sum_probs=20.8

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +||||.++.++..++++.-.++|..
T Consensus        14 aGKTT~~~~L~~~l~~~g~~v~~tr   38 (208)
T COG0125          14 AGKTTQAELLKERLEERGIKVVLTR   38 (208)
T ss_pred             CCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            6999999999999887766666665

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=82.87  E-value=3  Score=31.66  Aligned_cols=25  Identities=20%  Similarity=0.155  Sum_probs=22.6

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +|||+++.++..+...+...++|++
T Consensus        34 sGKT~f~~qfl~~~~~~ge~vlyvs   58 (260)
T COG0467          34 TGKTIFALQFLYEGAREGEPVLYVS   58 (260)
T ss_pred             CcHHHHHHHHHHHHHhcCCcEEEEE
Confidence            6999999999998777788899997

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

Probab=82.78  E-value=28  Score=30.98  Aligned_cols=141  Identities=16%  Similarity=0.199  Sum_probs=76.9

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhc-CCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRL-SRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l-~~~~~LlVlDdv~~   79 (192)
                      +|||-||+.++.+-.-     -|+++...             +.++.+.+...  ..++.+.... ...++.+-+|.++.
T Consensus       355 TGKTLLAKAiAGEAgV-----PF~svSGS-------------EFvE~~~g~~a--srvr~lf~~ar~~aP~iifideida  414 (774)
T KOG0731|consen  355 TGKTLLAKAIAGEAGV-----PFFSVSGS-------------EFVEMFVGVGA--SRVRDLFPLARKNAPSIIFIDEIDA  414 (774)
T ss_pred             CcHHHHHHHHhcccCC-----ceeeechH-------------HHHHHhcccch--HHHHHHHHHhhccCCeEEEeccccc
Confidence            5999999999987532     34442111             22222222111  0222233333 45689999998863


Q ss_pred             ch-----------------hHHHhhccCCCCCCCceEEE--EecchhHHhhc-----CCCceEecCCCCHHHHHHHHHHh
Q 039644           80 FS-----------------QLESLMGSLDWLTPVSRIIL--TTRNKQVLRNW-----GVSKIYEMEALEYHHALELFSQH  135 (192)
Q Consensus        80 ~~-----------------~~~~l~~~~~~~~~~~~iiv--TtR~~~~~~~~-----~~~~~~~l~~l~~~ea~~lf~~~  135 (192)
                      ..                 -+.++......+...+.||+  +|+..++....     .-...+.++.-+...-.++|..+
T Consensus       415 ~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~~~~~vi~~a~tnr~d~ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h  494 (774)
T KOG0731|consen  415 VGRKRGGKGTGGGQDEREQTLNQLLVEMDGFETSKGVIVLAATNRPDILDPALLRPGRFDRQIQIDLPDVKGRASILKVH  494 (774)
T ss_pred             ccccccccccCCCChHHHHHHHHHHHHhcCCcCCCcEEEEeccCCccccCHHhcCCCccccceeccCCchhhhHHHHHHH
Confidence            21                 14455544444444443443  45444433322     22455777777888888999888


Q ss_pred             hcCCCCCCccHHHHHHHHHHHhCCCchH
Q 039644          136 AFKRNHPDVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       136 ~~~~~~~~~~~~~~~~~i~~~~~g~Pla  163 (192)
                      +...+.. .+..++.+ +....-|++=|
T Consensus       495 ~~~~~~~-~e~~dl~~-~a~~t~gf~ga  520 (774)
T KOG0731|consen  495 LRKKKLD-DEDVDLSK-LASLTPGFSGA  520 (774)
T ss_pred             hhccCCC-cchhhHHH-HHhcCCCCcHH
Confidence            7544432 34455555 77777777755

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=82.61  E-value=1.2  Score=33.04  Aligned_cols=20  Identities=20%  Similarity=0.350  Sum_probs=16.1

Q ss_pred             CchhHHHHHHHHHhhCCCcc
Q 039644            1 IGKTAIARAIFDKISGDFEC   20 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~   20 (192)
                      +||||+|+.++..+......
T Consensus        19 SGKTTva~~l~~~~~~~~~~   38 (218)
T COG0572          19 SGKTTVAKELSEQLGVEKVV   38 (218)
T ss_pred             CCHHHHHHHHHHHhCcCcce
Confidence            69999999999988755333

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=82.55  E-value=21  Score=27.84  Aligned_cols=57  Identities=14%  Similarity=0.113  Sum_probs=36.5

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchhHH-hhc-CCCceEecCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQVL-RNW-GVSKIYEMEAL  123 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~~~-~~~-~~~~~~~l~~l  123 (192)
                      +..=++|+|+++...  ....+...+-+-..++.+|++|.+.... ... +....+.+.++
T Consensus        94 ~~~kv~ii~~ad~mt~~AaNaLLK~LEEPp~~~~fiL~~~~~~~ll~TI~SRcq~~~~~~~  154 (290)
T PRK05917         94 SPYKIYIIHEADRMTLDAISAFLKVLEDPPQHGVIILTSAKPQRLPPTIRSRSLSIHIPME  154 (290)
T ss_pred             CCceEEEEechhhcCHHHHHHHHHHhhcCCCCeEEEEEeCChhhCcHHHHhcceEEEccch
Confidence            445588999999764  4777777666666677777777764432 222 34455666644

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=82.51  E-value=0.8  Score=29.74  Aligned_cols=18  Identities=22%  Similarity=0.488  Sum_probs=14.8

Q ss_pred             CchhHHHHHHHHHhhCCC
Q 039644            1 IGKTAIARAIFDKISGDF   18 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F   18 (192)
                      +|||+||..++..+.+++
T Consensus         9 ~GKS~l~~~l~~~l~~~~   26 (107)
T PF00910_consen    9 IGKSTLAKELAKDLLKHI   26 (107)
T ss_pred             CCHHHHHHHHHHHHHHHh
Confidence            699999999999765544

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

>PRK09281 F0F1 ATP synthase subunit alpha; Validated

Probab=82.49  E-value=2.4  Score=35.59  Aligned_cols=14  Identities=36%  Similarity=0.525  Sum_probs=11.9

Q ss_pred             CceEEEEEeCCCCc
Q 039644           67 RMKVLIVFDDVTCF   80 (192)
Q Consensus        67 ~~~~LlVlDdv~~~   80 (192)
                      +++.|+|+||+...
T Consensus       253 G~~VLli~DdlTr~  266 (502)
T PRK09281        253 GKDALIVYDDLSKQ  266 (502)
T ss_pred             CCCEEEEecCchHH
Confidence            78999999999543

>PRK07413 hypothetical protein; Validated

Probab=82.38  E-value=10  Score=30.69  Aligned_cols=51  Identities=16%  Similarity=0.200  Sum_probs=31.9

Q ss_pred             hHHHHhhcCCceE-EEEEeCCCCch-----hHHHhhccCCCCCCCceEEEEecchhH
Q 039644           58 IDLNFRRLSRMKV-LIVFDDVTCFS-----QLESLMGSLDWLTPVSRIILTTRNKQV  108 (192)
Q Consensus        58 ~~~l~~~l~~~~~-LlVlDdv~~~~-----~~~~l~~~~~~~~~~~~iivTtR~~~~  108 (192)
                      .+..+..+.+..| |+|||.+..--     ..+.+...+.....+..||+|-|+...
T Consensus       114 ~~~a~~~i~sg~ydlvILDEi~~Al~~gll~~eevl~~L~~rP~~~evVLTGR~ap~  170 (382)
T PRK07413        114 WDIAKGAIASGLYSVVVLDELNPVLDLGLLPVDEVVNTLKSRPEGLEIIITGRAAPQ  170 (382)
T ss_pred             HHHHHHHHhCCCCCEEEEehhHHHHHCCCccHHHHHHHHHhCCCCCEEEEeCCCCCH
Confidence            3445555666666 99999996322     233444434444567799999998553

>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI

Probab=82.25  E-value=1.9  Score=35.34  Aligned_cols=74  Identities=18%  Similarity=0.161  Sum_probs=38.0

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHh--------cCCCC---cC-----chHHHHhh
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNIL--------KDKNV---MP-----YIDLNFRR   64 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~--------~~~~~---~~-----~~~~l~~~   64 (192)
                      +|||||+..++...+.. .+++.....+.     ..+.++....+..-.        ...++   ..     ..-.+.++
T Consensus       151 ~GKTtLl~~I~~~~~~~-~gvi~~iGer~-----~ev~~~~~~~l~~~~~~~tvvv~atsd~~~~~r~~a~~~a~~iAEy  224 (418)
T TIGR03498       151 VGKSTLLSMLARNTDAD-VVVIALVGERG-----REVREFLEDDLGEEGLKRSVVVVATSDESPLMRRQAAYTATAIAEY  224 (418)
T ss_pred             CChHHHHHHHhCCCCCC-EEEEEEEeeec-----hHHHHHHHHhhhccccceeEEEEECCCCCHHHHHHHHHHHHHHHHH
Confidence            59999998888765432 23333332222     345555544333211        00111   00     12223344


Q ss_pred             c--CCceEEEEEeCCCCc
Q 039644           65 L--SRMKVLIVFDDVTCF   80 (192)
Q Consensus        65 l--~~~~~LlVlDdv~~~   80 (192)
                      +  .+++.|+++||+...
T Consensus       225 frd~G~~Vll~~DslTr~  242 (418)
T TIGR03498       225 FRDQGKDVLLLMDSVTRF  242 (418)
T ss_pred             HHHcCCCEEEeccchhHH
Confidence            4  478999999999644

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>CHL00059 atpA ATP synthase CF1 alpha subunit

Probab=82.17  E-value=2.9  Score=34.89  Aligned_cols=15  Identities=27%  Similarity=0.472  Sum_probs=12.3

Q ss_pred             CCceEEEEEeCCCCc
Q 039644           66 SRMKVLIVFDDVTCF   80 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~   80 (192)
                      ++++.|+|+||+...
T Consensus       231 ~G~~VLlv~DdlTr~  245 (485)
T CHL00059        231 RGRHTLIIYDDLSKQ  245 (485)
T ss_pred             cCCCEEEEEcChhHH
Confidence            478999999999543

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=82.10  E-value=1.4  Score=32.76  Aligned_cols=45  Identities=9%  Similarity=0.018  Sum_probs=28.0

Q ss_pred             CceEEEEEeCCCCchh-------HHHhhccCCCCCCCceEEEEecchhHHhhc
Q 039644           67 RMKVLIVFDDVTCFSQ-------LESLMGSLDWLTPVSRIILTTRNKQVLRNW  112 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~~-------~~~l~~~~~~~~~~~~iivTtR~~~~~~~~  112 (192)
                      +.+-|++||.+.....       ...+...+... .++.+|++|....+....
T Consensus       109 ~~~sLvllDE~~~gT~~~d~~~i~~~il~~l~~~-~~~~~i~~TH~~~l~~~~  160 (222)
T cd03287         109 TSRSLVILDELGRGTSTHDGIAIAYATLHYLLEE-KKCLVLFVTHYPSLGEIL  160 (222)
T ss_pred             CCCeEEEEccCCCCCChhhHHHHHHHHHHHHHhc-cCCeEEEEcccHHHHHHH
Confidence            4689999999843221       12233333322 467899999988876544

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

>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=81.87  E-value=1.7  Score=31.11  Aligned_cols=16  Identities=25%  Similarity=0.414  Sum_probs=13.7

Q ss_pred             CchhHHHHHHHHHhhC
Q 039644            1 IGKTAIARAIFDKISG   16 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~   16 (192)
                      +||||||..+...+..
T Consensus        10 sGKttla~~l~~~l~~   25 (179)
T cd02028          10 SGKTTFAKKLSNQLRV   25 (179)
T ss_pred             CCHHHHHHHHHHHHHH
Confidence            6999999999997653

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>PF02463 SMC_N: RecF/RecN/SMC N terminal domain; InterPro: IPR003395 This domain is found at the N terminus of structural maintenance of chromosomes (SMC) proteins, which function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression []

Probab=81.82  E-value=1.2  Score=32.69  Aligned_cols=45  Identities=22%  Similarity=0.310  Sum_probs=27.2

Q ss_pred             ceEEEEEeCCCCch---hHHHhhccCCCCCCCceEEEEecchhHHhhc
Q 039644           68 MKVLIVFDDVTCFS---QLESLMGSLDWLTPVSRIILTTRNKQVLRNW  112 (192)
Q Consensus        68 ~~~LlVlDdv~~~~---~~~~l~~~~~~~~~~~~iivTtR~~~~~~~~  112 (192)
                      ..-++||||++..-   ....+...+......+.+||||..+.+....
T Consensus       158 ~~p~~ilDEvd~~LD~~~~~~l~~~l~~~~~~~Q~ii~Th~~~~~~~a  205 (220)
T PF02463_consen  158 PSPFLILDEVDAALDEQNRKRLADLLKELSKQSQFIITTHNPEMFEDA  205 (220)
T ss_dssp             --SEEEEESTTTTS-HHHHHHHHHHHHHHTTTSEEEEE-S-HHHHTT-
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            34589999998542   2444444444445568899999988877665

The domain is also found in RecF and RecN proteins, which are involved in DNA metabolism and recombination.; PDB: 3HTK_A 1W1W_C 2WD5_A 3L51_A 1XEW_Y 3KTA_B 3NWC_B 1XEX_A 1GXL_C 1GXK_A ....

>PF01202 SKI: Shikimate kinase; InterPro: IPR000623 Shikimate kinase (2

Probab=81.53  E-value=1  Score=31.45  Aligned_cols=17  Identities=12%  Similarity=0.401  Sum_probs=14.7

Q ss_pred             CchhHHHHHHHHHhhCC
Q 039644            1 IGKTAIARAIFDKISGD   17 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~   17 (192)
                      +||||+++.++..+.-.
T Consensus         3 sGKStvg~~lA~~L~~~   19 (158)
T PF01202_consen    3 SGKSTVGKLLAKRLGRP   19 (158)
T ss_dssp             SSHHHHHHHHHHHHTSE
T ss_pred             CcHHHHHHHHHHHhCCC
Confidence            69999999999988644

7.1.71 from EC) catalyses the fifth step in the biosynthesis of aromatic amino acids from chorismate (the so-called shikimate pathway) []. The enzyme catalyses the following reaction: ATP + shikimate = ADP + shikimate-3-phosphate The protein is found in bacteria (gene aroK or aroL), plants and fungi (where it is part of a multifunctional enzyme that catalyses five consecutive steps in this pathway). In 1994, the 3D structure of shikimate kinase was predicted to be very close to that of adenylate kinase, suggesting a functional similarity as well as an evolutionary relationship []. This prediction has since been confirmed experimentally. The protein is reported to possess an alpha/beta fold, consisting of a central sheet of five parallel beta-strands flanked by alpha-helices. Such a topology is very similar to that of adenylate kinase [].; GO: 0004765 shikimate kinase activity, 0005524 ATP binding; PDB: 3VAA_C 1KO8_B 1KO4_B 1KO1_A 1KOF_A 1KNQ_A 1KO5_A 1KAG_A 2PT5_D 1SHK_A ....

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=81.49  E-value=6.5  Score=32.53  Aligned_cols=74  Identities=16%  Similarity=0.127  Sum_probs=38.3

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHh--------cCCCC--cC------chHHHHhh
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNIL--------KDKNV--MP------YIDLNFRR   64 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~--------~~~~~--~~------~~~~l~~~   64 (192)
                      +|||||+.+++.....  +.+++.. +++-.   ..+.++....+..-.        ...++  ..      ..-.+.++
T Consensus       169 ~GKTtLL~~I~~~~~~--d~~v~~~-iGER~---rEv~ef~~~~l~~~~l~rsvvv~atsd~~~~~r~~a~~~a~tiAEy  242 (442)
T PRK08927        169 VGKSVLLSMLARNADA--DVSVIGL-IGERG---REVQEFLQDDLGPEGLARSVVVVATSDEPALMRRQAAYLTLAIAEY  242 (442)
T ss_pred             CCHHHHHHHHHhccCC--CEEEEEE-EecCc---HHHHHHHHHHhhccCceeEEEEEECCCCCHHHHHHHHHHHHHHHHH
Confidence            6999999999876543  2333332 33211   345555544433211        01111  00      12223333


Q ss_pred             c--CCceEEEEEeCCCCc
Q 039644           65 L--SRMKVLIVFDDVTCF   80 (192)
Q Consensus        65 l--~~~~~LlVlDdv~~~   80 (192)
                      +  .+++.|+++||+...
T Consensus       243 frd~G~~Vll~~DslTr~  260 (442)
T PRK08927        243 FRDQGKDVLCLMDSVTRF  260 (442)
T ss_pred             HHHCCCcEEEEEeCcHHH
Confidence            3  478999999999543

>PRK09099 type III secretion system ATPase; Provisional

Probab=81.38  E-value=2.4  Score=35.01  Aligned_cols=74  Identities=15%  Similarity=0.148  Sum_probs=38.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHh--------cCCCC--cC------chHHHHhh
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNIL--------KDKNV--MP------YIDLNFRR   64 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~--------~~~~~--~~------~~~~l~~~   64 (192)
                      +|||||++.++...... .+++....-+.     ..+.++...+...-.        ...++  ..      ..-.+.++
T Consensus       174 ~GKTtLl~~ia~~~~~d-~~vi~~iGer~-----~ev~ef~~~~~~~~~l~rtvvv~~tsd~p~~~r~~a~~~a~tiAEy  247 (441)
T PRK09099        174 VGKSTLMGMFARGTQCD-VNVIALIGERG-----REVREFIELILGEDGMARSVVVCATSDRSSIERAKAAYVATAIAEY  247 (441)
T ss_pred             CCHHHHHHHHhCCCCCC-eEEEEEEccCh-----HHHHHHHHHHhhcCCcceEEEEEECCCCCHHHHHHHHHHHHHHHHH
Confidence            59999999998754432 23444332222     345555444433211        00010  00      11223333


Q ss_pred             c--CCceEEEEEeCCCCc
Q 039644           65 L--SRMKVLIVFDDVTCF   80 (192)
Q Consensus        65 l--~~~~~LlVlDdv~~~   80 (192)
                      +  .+++.|+++||+...
T Consensus       248 frd~G~~VLl~~DslTr~  265 (441)
T PRK09099        248 FRDRGLRVLLMMDSLTRF  265 (441)
T ss_pred             HHHcCCCEEEeccchhHH
Confidence            3  478999999999644

>COG1485 Predicted ATPase [General function prediction only]

Probab=81.27  E-value=4.9  Score=32.09  Aligned_cols=89  Identities=13%  Similarity=0.188  Sum_probs=50.3

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCC--
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVT--   78 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~--   78 (192)
                      .|||.|.-.+|+.+...=...             ....+++..+-+.+.....+.+.+..+...+..+-.+|+||.+.  
T Consensus        76 rGKT~LMD~Fy~~lp~~~k~R-------------~HFh~FM~~vH~~l~~l~g~~dpl~~iA~~~~~~~~vLCfDEF~Vt  142 (367)
T COG1485          76 RGKTMLMDLFYESLPGERKRR-------------LHFHRFMARVHQRLHTLQGQTDPLPPIADELAAETRVLCFDEFEVT  142 (367)
T ss_pred             ccHHHHHHHHHhhCCcccccc-------------ccHHHHHHHHHHHHHHHcCCCCccHHHHHHHHhcCCEEEeeeeeec
Confidence            499999999999653211000             23345555555554433322346666677777777799999985  


Q ss_pred             Cchh---HHHhhccCCCCCCCceEEEEecc
Q 039644           79 CFSQ---LESLMGSLDWLTPVSRIILTTRN  105 (192)
Q Consensus        79 ~~~~---~~~l~~~~~~~~~~~~iivTtR~  105 (192)
                      +..+   +..+...+-  ..|. +||+|.|
T Consensus       143 DI~DAMiL~rL~~~Lf--~~GV-~lvaTSN  169 (367)
T COG1485         143 DIADAMILGRLLEALF--ARGV-VLVATSN  169 (367)
T ss_pred             ChHHHHHHHHHHHHHH--HCCc-EEEEeCC
Confidence            3222   445444442  3455 4444444

>PF07931 CPT: Chloramphenicol phosphotransferase-like protein; InterPro: IPR012853 The members of this family are all similar to chloramphenicol 3-O phosphotransferase (CPT, Q56148 from SWISSPROT) expressed by Streptomyces venezuelae

Probab=81.14  E-value=1.1  Score=32.10  Aligned_cols=15  Identities=40%  Similarity=0.731  Sum_probs=13.0

Q ss_pred             CchhHHHHHHHHHhh
Q 039644            1 IGKTAIARAIFDKIS   15 (192)
Q Consensus         1 iGKTtLa~~~~~~~~   15 (192)
                      +||||+|+.+.....
T Consensus        12 SGKSsia~~Lq~~~~   26 (174)
T PF07931_consen   12 SGKSSIARALQERLP   26 (174)
T ss_dssp             SSHHHHHHHHHHHSS
T ss_pred             CCHHHHHHHHHHhCc
Confidence            699999999998754

Chloramphenicol (Cm) is a metabolite produced by this bacterium that can inhibit ribosomal peptidyl transferase activity and therefore protein production. By transferring a phosphate group to the C-3 hydroxyl group of Cm, CPT inactivates this potentially lethal metabolite [, ]. ; GO: 0005524 ATP binding, 0016740 transferase activity; PDB: 1QHX_A 1QHN_A 1GRR_A 1QHY_A 1QHS_A 1GRQ_A.

>PRK08233 hypothetical protein; Provisional

Probab=80.95  E-value=1.1  Score=31.79  Aligned_cols=15  Identities=27%  Similarity=0.417  Sum_probs=13.0

Q ss_pred             CchhHHHHHHHHHhh
Q 039644            1 IGKTAIARAIFDKIS   15 (192)
Q Consensus         1 iGKTtLa~~~~~~~~   15 (192)
                      +||||||..++..+.
T Consensus        14 sGKtTla~~L~~~l~   28 (182)
T PRK08233         14 GGKTTLTERLTHKLK   28 (182)
T ss_pred             CCHHHHHHHHHhhCC
Confidence            699999999998764

>PTZ00185 ATPase alpha subunit; Provisional

Probab=80.85  E-value=11  Score=32.11  Aligned_cols=15  Identities=27%  Similarity=0.366  Sum_probs=12.4

Q ss_pred             CCceEEEEEeCCCCc
Q 039644           66 SRMKVLIVFDDVTCF   80 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~   80 (192)
                      ++++.|+|+||+...
T Consensus       287 ~GkdVLiv~DDLTr~  301 (574)
T PTZ00185        287 RGRHCLCVYDDLSKQ  301 (574)
T ss_pred             cCCCEEEEEcCchHH
Confidence            478999999999643

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=80.84  E-value=2.1  Score=29.30  Aligned_cols=25  Identities=20%  Similarity=0.209  Sum_probs=19.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +|||+++..++......-..++|++
T Consensus        10 ~GKT~l~~~i~~~~~~~~~~v~~~~   34 (165)
T cd01120          10 SGKTTLALQLALNIATKGGKVVYVD   34 (165)
T ss_pred             CCHHHHHHHHHHHHHhcCCEEEEEE
Confidence            5999999999997655445566775

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.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=80.66  E-value=25  Score=29.09  Aligned_cols=17  Identities=18%  Similarity=0.100  Sum_probs=13.6

Q ss_pred             CchhHHHHHHHHHhhCC
Q 039644            1 IGKTAIARAIFDKISGD   17 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~   17 (192)
                      +||||++..++..++.+
T Consensus       111 vGKTTtaaKLA~~l~~~  127 (429)
T TIGR01425       111 SGKTTTCTKLAYYYQRK  127 (429)
T ss_pred             CCHHHHHHHHHHHHHHC
Confidence            69999999998865443

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.

>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=80.62  E-value=1.2  Score=30.21  Aligned_cols=14  Identities=36%  Similarity=0.551  Sum_probs=13.2

Q ss_pred             CchhHHHHHHHHHh
Q 039644            1 IGKTAIARAIFDKI   14 (192)
Q Consensus         1 iGKTtLa~~~~~~~   14 (192)
                      +|||+||+.+++.+
T Consensus        10 ~GKt~l~~~la~~~   23 (139)
T PF07728_consen   10 TGKTTLARELAALL   23 (139)
T ss_dssp             SSHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHh
Confidence            69999999999988

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.

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=80.61  E-value=1.3  Score=31.37  Aligned_cols=15  Identities=40%  Similarity=0.623  Sum_probs=13.0

Q ss_pred             CchhHHHHHHHHHhh
Q 039644            1 IGKTAIARAIFDKIS   15 (192)
Q Consensus         1 iGKTtLa~~~~~~~~   15 (192)
                      +||||+|+.+.....
T Consensus        13 sGKst~a~~l~~~~~   27 (175)
T cd00227          13 AGKSSIARALQSVLA   27 (175)
T ss_pred             CCHHHHHHHHHHhhC
Confidence            699999999998754

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=80.55  E-value=1.2  Score=29.91  Aligned_cols=14  Identities=29%  Similarity=0.501  Sum_probs=12.1

Q ss_pred             CchhHHHHHHHHHh
Q 039644            1 IGKTAIARAIFDKI   14 (192)
Q Consensus         1 iGKTtLa~~~~~~~   14 (192)
                      .||||+++.++..+
T Consensus        26 aGKTtf~r~l~~~l   39 (123)
T PF02367_consen   26 AGKTTFVRGLARAL   39 (123)
T ss_dssp             SSHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHc
Confidence            59999999999953

They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.

>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]

Probab=80.45  E-value=1.2  Score=31.47  Aligned_cols=24  Identities=17%  Similarity=0.155  Sum_probs=18.6

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEE
Q 039644            1 IGKTAIARAIFDKISGDFECSCFL   24 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv   24 (192)
                      +|||||..++..+++++--.+.-+
T Consensus        13 SGKTTLie~lv~~L~~~G~rVa~i   36 (161)
T COG1763          13 SGKTTLIEKLVRKLKARGYRVATV   36 (161)
T ss_pred             CChhhHHHHHHHHHHhCCcEEEEE
Confidence            699999999999987765444444

>PF02223 Thymidylate_kin: Thymidylate kinase; InterPro: IPR018094 Thymidylate kinase (2

Probab=80.31  E-value=3.4  Score=29.47  Aligned_cols=20  Identities=20%  Similarity=0.112  Sum_probs=16.4

Q ss_pred             CchhHHHHHHHHHhhCCCcc
Q 039644            1 IGKTAIARAIFDKISGDFEC   20 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~   20 (192)
                      +||||+++.+++.+......
T Consensus         7 sGKtT~~~~L~~~l~~~~~~   26 (186)
T PF02223_consen    7 SGKTTQIRLLAEALKEKGYK   26 (186)
T ss_dssp             SSHHHHHHHHHHHHHHTTEE
T ss_pred             CCHHHHHHHHHHHHHHcCCc
Confidence            69999999999987766433

7.4.9 from EC; dTMP kinase) catalyzes the phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) in the presence of ATP and magnesium: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate Thymidylate kinase is an ubiquitous enzyme of about 25 Kd and is important in the dTTP synthesis pathway for DNA synthesis. The function of dTMP kinase in eukaryotes comes from the study of a cell cycle mutant, cdc8, in Saccharomyces cerevisiae. Structural and functional analyses suggest that the cDNA codes for authentic human dTMP kinase. The mRNA levels and enzyme activities corresponded to cell cycle progression and cell growth stages[]. ; GO: 0004798 thymidylate kinase activity, 0005524 ATP binding, 0006233 dTDP biosynthetic process; PDB: 2PLR_B 1NMX_A 1NN0_A 2XX3_A 1NN3_A 1E9F_A 1E2Q_A 1E2D_A 1E9A_A 1E99_A ....

>COG3172 NadR Predicted ATPase/kinase involved in NAD metabolism [Coenzyme metabolism]

Probab=80.22  E-value=1.4  Score=31.12  Aligned_cols=17  Identities=12%  Similarity=0.282  Sum_probs=14.2

Q ss_pred             CchhHHHHHHHHHhhCC
Q 039644            1 IGKTAIARAIFDKISGD   17 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~   17 (192)
                      +||||||++++..+...
T Consensus        19 sGKStLv~kLA~~fnt~   35 (187)
T COG3172          19 SGKSTLVNKLANIFNTT   35 (187)
T ss_pred             cChHHHHHHHHHHhCCC
Confidence            59999999999976543

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

Probab=80.16  E-value=33  Score=28.50  Aligned_cols=85  Identities=15%  Similarity=0.156  Sum_probs=45.4

Q ss_pred             ceEEE-EecchhHHhhc----CC-CceEecCCCCHHHHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCCchHHHHHHH-
Q 039644           97 SRIIL-TTRNKQVLRNW----GV-SKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSC-  169 (192)
Q Consensus        97 ~~iiv-TtR~~~~~~~~----~~-~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plai~~~~~-  169 (192)
                      =|||| ||....-..+.    |. ..-+.|+.-+...-..|+.++..... +++    +..+|.+...+.-+.=+.+++ 
T Consensus       338 ERIivFTTNh~EkLDPALlRpGRmDmhI~mgyCtf~~fK~La~nYL~~~~-~h~----L~~eie~l~~~~~~tPA~V~e~  412 (457)
T KOG0743|consen  338 ERIIVFTTNHKEKLDPALLRPGRMDMHIYMGYCTFEAFKTLASNYLGIEE-DHR----LFDEIERLIEETEVTPAQVAEE  412 (457)
T ss_pred             ceEEEEecCChhhcCHhhcCCCcceeEEEcCCCCHHHHHHHHHHhcCCCC-Ccc----hhHHHHHHhhcCccCHHHHHHH
Confidence            35555 66654433222    22 23467888888888888888764422 233    344455555566555455555 


Q ss_pred             HhccC-C-HHHHHHHHHHH
Q 039644          170 FLHKR-E-KEVWESAIDKL  186 (192)
Q Consensus       170 ~l~~~-~-~~~w~~~l~~l  186 (192)
                      +|..+ + ....+.+.+.+
T Consensus       413 lm~~~~dad~~lk~Lv~~l  431 (457)
T KOG0743|consen  413 LMKNKNDADVALKGLVEAL  431 (457)
T ss_pred             HhhccccHHHHHHHHHHHH
Confidence            55555 3 33334444433

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=80.12  E-value=27  Score=27.40  Aligned_cols=69  Identities=16%  Similarity=0.284  Sum_probs=48.3

Q ss_pred             CceEEEEEeCCCCchh--HHHhhccCCCCCCCceEEEEecchh-HHhh-cCCCceEecCCCCHHHHHHHHHHh
Q 039644           67 RMKVLIVFDDVTCFSQ--LESLMGSLDWLTPVSRIILTTRNKQ-VLRN-WGVSKIYEMEALEYHHALELFSQH  135 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~~--~~~l~~~~~~~~~~~~iivTtR~~~-~~~~-~~~~~~~~l~~l~~~ea~~lf~~~  135 (192)
                      +.+=++|+|+++....  ...+...+.+...++.+|++|.+.. +... .+....+++.+++.++..+.+...
T Consensus        89 ~~~KvvII~~~e~m~~~a~NaLLK~LEEPp~~t~~il~~~~~~kll~TI~SRc~~~~f~~l~~~~l~~~l~~~  161 (299)
T PRK07132         89 SQKKILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQVFNVKEPDQQKILAKLLSK  161 (299)
T ss_pred             CCceEEEEecccccCHHHHHHHHHHhhCCCCCeEEEEEeCChHhChHHHHhCeEEEECCCCCHHHHHHHHHHc
Confidence            4667899999986643  6677777766667777777665433 3322 255788999999999988776553

>PRK10867 signal recognition particle protein; Provisional

Probab=80.12  E-value=26  Score=29.05  Aligned_cols=17  Identities=24%  Similarity=0.270  Sum_probs=13.4

Q ss_pred             CchhHHHHHHHHHhhCC
Q 039644            1 IGKTAIARAIFDKISGD   17 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~   17 (192)
                      +||||++..++..+...
T Consensus       111 sGKTTtaakLA~~l~~~  127 (433)
T PRK10867        111 AGKTTTAGKLAKYLKKK  127 (433)
T ss_pred             CcHHHHHHHHHHHHHHh
Confidence            69999999988865544

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

Probab=80.04  E-value=11  Score=29.14  Aligned_cols=137  Identities=18%  Similarity=0.180  Sum_probs=69.8

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhc-CCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRL-SRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l-~~~~~LlVlDdv~~   79 (192)
                      .|||-+|+.+++..+.-|     +. +        ...+++   .+.++....   .+.++.... +.-+|++.||.++.
T Consensus       162 TGKTm~Akalane~kvp~-----l~-v--------kat~li---GehVGdgar---~Ihely~rA~~~aPcivFiDE~DA  221 (368)
T COG1223         162 TGKTMMAKALANEAKVPL-----LL-V--------KATELI---GEHVGDGAR---RIHELYERARKAAPCIVFIDELDA  221 (368)
T ss_pred             ccHHHHHHHHhcccCCce-----EE-e--------chHHHH---HHHhhhHHH---HHHHHHHHHHhcCCeEEEehhhhh
Confidence            499999999999765432     22 1        222222   222221111   233333333 34699999999863


Q ss_pred             ch--------------hHHHhhccCCCC--CCCceEEEEecchhHHhhc---CCCceEecCCCCHHHHHHHHHHhhcCCC
Q 039644           80 FS--------------QLESLMGSLDWL--TPVSRIILTTRNKQVLRNW---GVSKIYEMEALEYHHALELFSQHAFKRN  140 (192)
Q Consensus        80 ~~--------------~~~~l~~~~~~~--~~~~~iivTtR~~~~~~~~---~~~~~~~l~~l~~~ea~~lf~~~~~~~~  140 (192)
                      ..              ..+.+...+...  +.|..-|-.|.+.......   ...+.++...-+.+|-.+++..++-.-.
T Consensus       222 iaLdRryQelRGDVsEiVNALLTelDgi~eneGVvtIaaTN~p~~LD~aiRsRFEeEIEF~LP~~eEr~~ile~y~k~~P  301 (368)
T COG1223         222 IALDRRYQELRGDVSEIVNALLTELDGIKENEGVVTIAATNRPELLDPAIRSRFEEEIEFKLPNDEERLEILEYYAKKFP  301 (368)
T ss_pred             hhhhhhHHHhcccHHHHHHHHHHhccCcccCCceEEEeecCChhhcCHHHHhhhhheeeeeCCChHHHHHHHHHHHHhCC
Confidence            21              134444444332  2444455556555544332   2345566666688888888888763222


Q ss_pred             CCCccHHHHHHHHHHHhCCC
Q 039644          141 HPDVGYEKLSSNVTKYAQGI  160 (192)
Q Consensus       141 ~~~~~~~~~~~~i~~~~~g~  160 (192)
                      -+.   +...+.++++.+|+
T Consensus       302 lpv---~~~~~~~~~~t~g~  318 (368)
T COG1223         302 LPV---DADLRYLAAKTKGM  318 (368)
T ss_pred             Ccc---ccCHHHHHHHhCCC
Confidence            111   11234455555555

---

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	192
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	5e-19
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	2e-18
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-15
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	4e-10

>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 = 82.7 bits (204), Expect = 5e-19
 Identities = 32/204 (15%), Positives = 67/204 (32%), Gaps = 25/204 (12%)

Query: 1   IGKTAIARAIF---DKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPY 57
            GK+ IA       D++ G    S         + +      L   +L  +  + +++ +
Sbjct: 163 SGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPK--STFDLFTDILLMLKSEDDLLNF 220

Query: 58  ------------IDLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRN 105
                         +    + R   L VFDDV    Q E++           R ++TTR+
Sbjct: 221 PSVEHVTSVVLKRMICNALIDRPNTLFVFDDV---VQEETI---RWAQELRLRCLVTTRD 274

Query: 106 KQVLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLAL 164
            ++        +  E+ +LE     +    +       +   E + +   + + G P  L
Sbjct: 275 VEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEK-EEDVLNKTIELSSGNPATL 333

Query: 165 KVLSCFLHKREKEVWESAIDKLQR 188
            +       +  E      +KL+ 
Sbjct: 334 MMFFKSCEPKTFEKMAQLNNKLES 357

>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 = 81.0 bits (200), Expect = 2e-18
 Identities = 40/205 (19%), Positives = 73/205 (35%), Gaps = 28/205 (13%)

Query: 1   IGKTAIARAIF---DKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPY 57
            GK+ +A         + G F       +V  +  + G L  L+  L + + +D++    
Sbjct: 158 CGKSVLAAEAVRDHSLLEGCFPGGVHWVSV-GKQDKSGLLMKLQ-NLCTRLDQDESFSQR 215

Query: 58  IDLNFRRLSRM----------KVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQ 107
           + LN                 + L++ DDV            L       +I+LTTR+K 
Sbjct: 216 LPLNIEEAKDRLRILMLRKHPRSLLILDDV-------WDSWVLKAFDSQCQILLTTRDKS 268

Query: 108 VLRNWGVSK--IYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALK 165
           V  +    K  +    +L     LE+ S         D    + + ++ K  +G PL + 
Sbjct: 269 VTDSVMGPKYVVPVESSLGKEKGLEILSLFVN-MKKAD--LPEQAHSIIKECKGSPLVVS 325

Query: 166 VLSCFLHKREKEVWESAIDKLQRIL 190
           ++   L       WE  + +LQ   
Sbjct: 326 LIGALLRDFPNR-WEYYLKQLQNKQ 349

>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 = 73.3 bits (179), Expect = 1e-15
 Identities = 39/217 (17%), Positives = 69/217 (31%), Gaps = 45/217 (20%)

Query: 1   IGKTAIARAI--FDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYI 58
            GKT +A  +    K+    +   F  N++     P  +  + QKLL  I  +       
Sbjct: 161 SGKTWVALDVCLSYKVQCKMDFKIFWLNLKNC-NSPETVLEMLQKLLYQIDPNWTSRSDH 219

Query: 59  DLNFR--------RLSRM-------KVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTT 103
             N +         L R+         L+V  +V   ++        +      +I+LTT
Sbjct: 220 SSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNV-QNAKA------WNAFNLSCKILLTT 272

Query: 104 RNKQVLRNWGVSKIYEM------EALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYA 157
           R KQV      +    +        L       L  ++       D   + L   V    
Sbjct: 273 RFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYL------DCRPQDLPREVLT-- 324

Query: 158 QGIPLALKVLSCFLHKREKEVWE----SAIDKLQRIL 190
              P  L +++  + +     W+       DKL  I+
Sbjct: 325 -TNPRRLSIIAESI-RDGLATWDNWKHVNCDKLTTII 359

>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 = 57.1 bits (138), Expect = 4e-10
 Identities = 39/203 (19%), Positives = 72/203 (35%), Gaps = 28/203 (13%)

Query: 1   IGKTAIARAI---FDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPY 57
            GK+ +A         + G F       ++ +  Q   GL    Q L   + ++++    
Sbjct: 158 CGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGK--QDKSGLLMKLQNLCMRLDQEESFSQR 215

Query: 58  IDLNFR----RLSRM------KVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQ 107
           + LN      RL  +      + L++ DDV     +      L       +I+LTTR+K 
Sbjct: 216 LPLNIEEAKDRLRVLMLRKHPRSLLILDDV-WDPWV------LKAFDNQCQILLTTRDKS 268

Query: 108 VLRNW--GVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALK 165
           V  +       +     L     LE+ S      N         + ++ K  +G PL + 
Sbjct: 269 VTDSVMGPKHVVPVESGLGREKGLEILSLFV---NMKKEDLPAEAHSIIKECKGSPLVVS 325

Query: 166 VLSCFLHKREKEVWESAIDKLQR 188
           ++   L +     W   + +LQ 
Sbjct: 326 LIGALL-RDFPNRWAYYLRQLQN 347

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	192
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	99.96
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	99.92
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	99.89
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	99.87
2fna_A	357	Conserved hypothetical protein; structural genomic	99.16
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.14
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.11
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.97
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	98.96
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.79
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.7
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	98.69
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	98.66
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.46
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.23
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.22
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	98.08
2chq_A	319	Replication factor C small subunit; DNA-binding pr	98.05
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	98.01
3bos_A	242	Putative DNA replication factor; P-loop containing	97.98
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	97.91
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	97.71
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	97.65
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.6
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	97.59
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	97.46
3pvs_A	447	Replication-associated recombination protein A; ma	97.42
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	97.41
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	97.39
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	97.38
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	97.38
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	97.37
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	97.33
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	97.29
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	97.28
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	97.17
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	97.15
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	97.15
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	97.1
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	96.99
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	96.93
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	96.86
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	96.86
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.66
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	96.58
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	96.53
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	96.27
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	96.22
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	96.09
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	95.97
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	95.73
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	95.63
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	95.61
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	95.59
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	95.59
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	95.17
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	95.16
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	95.13
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	95.11
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	94.66
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	94.61
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	94.53
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	94.51
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	94.48
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	94.46
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	94.37
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	94.35
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	94.1
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	93.93
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	93.47
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	92.79
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	92.25
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	92.16
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	92.02
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	91.83
2cvh_A	220	DNA repair and recombination protein RADB; filamen	91.73
2qgz_A	308	Helicase loader, putative primosome component; str	91.43
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	91.36
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	91.14
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	89.7
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	89.7
3co5_A	143	Putative two-component system transcriptional RES	89.67
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	89.5
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	89.06
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	88.65
3ice_A	422	Transcription termination factor RHO; transcriptio	87.66
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	87.16
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	86.87
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	85.77
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	85.6
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	84.89
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	84.39
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	84.18
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	84.14
3l0o_A	427	Transcription termination factor RHO; helicase, RH	83.61
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	82.74
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	82.59
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	82.47
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	81.72
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	81.2
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	81.18
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	81.14
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	80.88
3oaa_A	513	ATP synthase subunit alpha; rossmann fold, hydrola	80.46
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	80.27
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	80.13

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*

Probab=99.96  E-value=1.2e-28  Score=203.98  Aligned_cols=165  Identities=16%  Similarity=0.185  Sum_probs=135.0

Q ss_pred             CchhHHHHHHHH----HhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCC--C---cC------chHHHHhhc
Q 039644            1 IGKTAIARAIFD----KISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKN--V---MP------YIDLNFRRL   65 (192)
Q Consensus         1 iGKTtLa~~~~~----~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~--~---~~------~~~~l~~~l   65 (192)
                      +||||||+++|+    +++.+|++++|++ ++..+.  ++..+++..++.++.....  .   .+      ....++..+
T Consensus       163 vGKTtLA~~v~~~~~~~~~~~F~~~~wv~-vs~~~~--~~~~~~~~~il~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L  239 (549)
T 2a5y_B          163 SGKSVIASQALSKSDQLIGINYDSIVWLK-DSGTAP--KSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNAL  239 (549)
T ss_dssp             SSHHHHHHHHHHHCSSTBTTTBSEEEEEE-CCCCST--THHHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhhhHHHhccCCcEEEEE-ECCCCC--CCHHHHHHHHHHHHhcCcccccccccccccHHHHHHHHHHHH
Confidence            799999999996    6899999999997 544211  3688999999999986532  1   11      368889999


Q ss_pred             CCc-eEEEEEeCCCCchhHHHhhccCCCCCCCceEEEEecchhHHhhcC-CCceEecCCCCHHHHHHHHHHhhcCCCCCC
Q 039644           66 SRM-KVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWG-VSKIYEMEALEYHHALELFSQHAFKRNHPD  143 (192)
Q Consensus        66 ~~~-~~LlVlDdv~~~~~~~~l~~~~~~~~~~~~iivTtR~~~~~~~~~-~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~  143 (192)
                      .++ ||||||||+|+..++ .+..     .+||+||||||++.++..++ ....+++++|+.++|++||.+.++.... .
T Consensus       240 ~~~kr~LlVLDdv~~~~~~-~~~~-----~~gs~ilvTTR~~~v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~-~  312 (549)
T 2a5y_B          240 IDRPNTLFVFDDVVQEETI-RWAQ-----ELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPV-G  312 (549)
T ss_dssp             TTSTTEEEEEEEECCHHHH-HHHH-----HTTCEEEEEESBGGGGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC---
T ss_pred             cCCCcEEEEEECCCCchhh-cccc-----cCCCEEEEEcCCHHHHHHcCCCCeEEECCCCCHHHHHHHHHHHhcCCCC-c
Confidence            996 999999999998765 2221     27899999999999988775 4467999999999999999999876543 4


Q ss_pred             ccHHHHHHHHHHHhCCCchHHHHHHHHhccCC
Q 039644          144 VGYEKLSSNVTKYAQGIPLALKVLSCFLHKRE  175 (192)
Q Consensus       144 ~~~~~~~~~i~~~~~g~Plai~~~~~~l~~~~  175 (192)
                      +.+.+.+.+|+++|+|+||||+++|+.|+.+.
T Consensus       313 ~~~~~~~~~I~~~c~GlPLAl~~~g~~l~~~~  344 (549)
T 2a5y_B          313 EKEEDVLNKTIELSSGNPATLMMFFKSCEPKT  344 (549)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSSS
T ss_pred             hhHHHHHHHHHHHhCCChHHHHHHHHHhccch
Confidence            67788999999999999999999999998874

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A*

Probab=99.92  E-value=1.6e-24  Score=192.88  Aligned_cols=176  Identities=21%  Similarity=0.304  Sum_probs=132.2

Q ss_pred             CchhHHHHHHHHH---hhCCCc-ceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC--------cCchHHHHhhcCCc
Q 039644            1 IGKTAIARAIFDK---ISGDFE-CSCFLENVREESQRPGGLACLRQKLLSNILKDKNV--------MPYIDLNFRRLSRM   68 (192)
Q Consensus         1 iGKTtLa~~~~~~---~~~~F~-~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--------~~~~~~l~~~l~~~   68 (192)
                      +||||||++++++   ...+|. .++|+. ++....  ......+..++..+......        .+....++..+.++
T Consensus       158 ~GKTtLa~~~~~~~~~~~~~~~~~~~~v~-~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~  234 (1249)
T 3sfz_A          158 CGKSVLAAEAVRDHSLLEGCFSGGVHWVS-IGKQDK--SGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRK  234 (1249)
T ss_dssp             SSHHHHHHHHTCCHHHHTTTSTTCEEEEE-CCSCCH--HHHHHHHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSS
T ss_pred             CCHHHHHHHHhcChhHHHhhCCCeEEEEE-ECCcCc--hHHHHHHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhcc
Confidence            7999999999996   456675 555877 433111  23444556666666544321        11666777777766


Q ss_pred             --eEEEEEeCCCCchhHHHhhccCCCCCCCceEEEEecchhHHhh-cCCCceEecCC-CCHHHHHHHHHHhhcCCCCCCc
Q 039644           69 --KVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRN-WGVSKIYEMEA-LEYHHALELFSQHAFKRNHPDV  144 (192)
Q Consensus        69 --~~LlVlDdv~~~~~~~~l~~~~~~~~~~~~iivTtR~~~~~~~-~~~~~~~~l~~-l~~~ea~~lf~~~~~~~~~~~~  144 (192)
                        ||||||||+|+..+|..+       ++|++||||||++.++.. .+....+.+++ |+.++|++||...++...   +
T Consensus       235 ~~~~LlvlDd~~~~~~~~~~-------~~~~~ilvTtR~~~~~~~~~~~~~~~~~~~~l~~~~a~~l~~~~~~~~~---~  304 (1249)
T 3sfz_A          235 HPRSLLILDDVWDPWVLKAF-------DNQCQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKK---E  304 (1249)
T ss_dssp             SCSCEEEEESCCCHHHHTTT-------CSSCEEEEEESSTTTTTTCCSCBCCEECCSSCCHHHHHHHHHHHHTSCS---T
T ss_pred             CCCEEEEEecCCCHHHHHhh-------cCCCEEEEEcCCHHHHHhhcCCceEEEecCCCCHHHHHHHHHHhhCCCh---h
Confidence              999999999998776654       578999999999988854 35667899996 999999999998874332   3


Q ss_pred             cHHHHHHHHHHHhCCCchHHHHHHHHhccCCHHHHHHHHHHHHhcC
Q 039644          145 GYEKLSSNVTKYAQGIPLALKVLSCFLHKREKEVWESAIDKLQRIL  190 (192)
Q Consensus       145 ~~~~~~~~i~~~~~g~Plai~~~~~~l~~~~~~~w~~~l~~l~~~~  190 (192)
                      ...+.+.+|+++|+|+||||+++|++|+.+. ..|..+++.+.+..
T Consensus       305 ~~~~~~~~i~~~~~glPLal~~~~~~l~~~~-~~~~~~l~~l~~~~  349 (1249)
T 3sfz_A          305 DLPAEAHSIIKECKGSPLVVSLIGALLRDFP-NRWAYYLRQLQNKQ  349 (1249)
T ss_dssp             TCCTHHHHHHHHTTTCHHHHHHHHHHHHHSS-SCHHHHHHHHHSCC
T ss_pred             hCcHHHHHHHHHhCCCHHHHHHHHHHhhcCh-hHHHHHHHHHhhhh
Confidence            3445688999999999999999999999875 57999998887543

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=99.89  E-value=1e-22  Score=175.18  Aligned_cols=160  Identities=17%  Similarity=0.151  Sum_probs=116.2

Q ss_pred             CchhHHHHHHHH--HhhCCCcc-eEEEeeccccccCCCChHHHHHHHHHHHhcCC----CC--c--C-------chHHHH
Q 039644            1 IGKTAIARAIFD--KISGDFEC-SCFLENVREESQRPGGLACLRQKLLSNILKDK----NV--M--P-------YIDLNF   62 (192)
Q Consensus         1 iGKTtLa~~~~~--~~~~~F~~-~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~----~~--~--~-------~~~~l~   62 (192)
                      +||||||+++++  +++.+|+. ++|++ ++..    ++...+...++..+....    ..  .  +       ....++
T Consensus       161 IGKTTLAk~Vy~d~rV~~~Fd~gV~WVs-Vs~~----~d~~~IL~~Ll~lL~~i~~~~~~~~d~~~~ip~~leeL~e~Lr  235 (1221)
T 1vt4_I          161 SGKTWVALDVCLSYKVQCKMDFKIFWLN-LKNC----NSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELR  235 (1221)
T ss_dssp             SSHHHHHHHHHHHCHHHHHHSSCEEEEE-CCCS----SSHHHHHHHHHHHHHHHCSSSTTTSCCCSSHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHhhHHHHhCCCcEEEEE-eCCC----CCHHHHHHHHHHHHhhcCcccccccccccCCCCCHHHHHHHHH
Confidence            799999999997  47889986 88988 4432    566677777666433211    00  0  0       345566


Q ss_pred             hhc---CCceEEEEEeCCCCchhHHHhhccCCCCCCCceEEEEecchhHHhhcCCCceEecC------CCCHHHHHHHHH
Q 039644           63 RRL---SRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEME------ALEYHHALELFS  133 (192)
Q Consensus        63 ~~l---~~~~~LlVlDdv~~~~~~~~l~~~~~~~~~~~~iivTtR~~~~~~~~~~~~~~~l~------~l~~~ea~~lf~  133 (192)
                      ..+   .++|+||||||+|+...|+.+.       +||+||||||++.++..+.....+.++      +|+.+||++||.
T Consensus       236 ~lL~~l~~KRvLLVLDDVwd~eqLe~f~-------pGSRILVTTRd~~Va~~l~g~~vy~LeL~d~dL~LS~eEA~eLF~  308 (1221)
T 1vt4_I          236 RLLKSKPYENCLLVLLNVQNAKAWNAFN-------LSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLL  308 (1221)
T ss_dssp             HHHHHSTTSSCEEEEESCCCHHHHHHHH-------SSCCEEEECSCSHHHHHHHHHSSCEEEECSSSSCCCHHHHHHHHH
T ss_pred             HHHHhhcCCCEEEEEeCcChHHHHHhhC-------CCeEEEEeccChHHHHhcCCCeEEEecCccccCCcCHHHHHHHHH
Confidence            654   6899999999999988888763       689999999999988644333345566      899999999999


Q ss_pred             HhhcCCCCCCccHHHHHHHHHHHhCCCchHHHHHHHHhccC--CHHHHHH
Q 039644          134 QHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKR--EKEVWES  181 (192)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~i~~~~~g~Plai~~~~~~l~~~--~~~~w~~  181 (192)
                      ..... .  .   .+...++   |+|+||||.++|+.|+.+  ....|+.
T Consensus       309 ~~~g~-~--~---eeL~~eI---CgGLPLALkLaGs~Lr~k~~s~eeW~~  349 (1221)
T 1vt4_I          309 KYLDC-R--P---QDLPREV---LTTNPRRLSIIAESIRDGLATWDNWKH  349 (1221)
T ss_dssp             HHHCC-C--T---TTHHHHH---CCCCHHHHHHHHHHHHHSCSSHHHHHH
T ss_pred             HHcCC-C--H---HHHHHHH---hCCCHHHHHHHHHHHhCCCCCHHHHhc
Confidence            88422 2  1   1223333   999999999999999987  3778864

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=99.87  E-value=4.3e-22  Score=165.97  Aligned_cols=171  Identities=22%  Similarity=0.282  Sum_probs=121.3

Q ss_pred             CchhHHHHHHHHHh---hCCCc-ceEEEeeccccccCCCChHHHHHHH---HHHHhcCCC---C--c---CchHHHHhhc
Q 039644            1 IGKTAIARAIFDKI---SGDFE-CSCFLENVREESQRPGGLACLRQKL---LSNILKDKN---V--M---PYIDLNFRRL   65 (192)
Q Consensus         1 iGKTtLa~~~~~~~---~~~F~-~~~wv~~~~~~~~~~~~~~~~~~~l---~~~~~~~~~---~--~---~~~~~l~~~l   65 (192)
                      +||||||.+++++.   ..+|+ .++|++. +.     .+...+...+   ...+.....   .  .   .....+...+
T Consensus       158 iGKTtLa~~~~~~~~~~~~~f~~~v~wv~~-~~-----~~~~~~~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l  231 (591)
T 1z6t_A          158 CGKSVLAAEAVRDHSLLEGCFPGGVHWVSV-GK-----QDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILM  231 (591)
T ss_dssp             SSHHHHHHHHHCCHHHHHHHCTTCEEEEEE-ES-----CCHHHHHHHHHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHhchhHHHhhCCCceEEEEC-CC-----CchHHHHHHHHHHHHHhccccccccCCCCCHHHHHHHHHHHH
Confidence            79999999999853   77895 7888873 33     1223333333   334432111   1  1   1455666666


Q ss_pred             CC--ceEEEEEeCCCCchhHHHhhccCCCCCCCceEEEEecchhHHhhcCCCceEec---CCCCHHHHHHHHHHhhcCCC
Q 039644           66 SR--MKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEM---EALEYHHALELFSQHAFKRN  140 (192)
Q Consensus        66 ~~--~~~LlVlDdv~~~~~~~~l~~~~~~~~~~~~iivTtR~~~~~~~~~~~~~~~l---~~l~~~ea~~lf~~~~~~~~  140 (192)
                      .+  +++||||||+|+...++.+       +++++||||||...+..... ...+.+   ++|+.+++++||...++.. 
T Consensus       232 ~~~~~~~LLVLDdv~~~~~l~~l-------~~~~~ilvTsR~~~~~~~~~-~~~~~v~~l~~L~~~ea~~L~~~~~~~~-  302 (591)
T 1z6t_A          232 LRKHPRSLLILDDVWDSWVLKAF-------DSQCQILLTTRDKSVTDSVM-GPKYVVPVESSLGKEKGLEILSLFVNMK-  302 (591)
T ss_dssp             HHTCTTCEEEEEEECCHHHHHTT-------CSSCEEEEEESCGGGGTTCC-SCEEEEECCSSCCHHHHHHHHHHHHTSC-
T ss_pred             ccCCCCeEEEEeCCCCHHHHHHh-------cCCCeEEEECCCcHHHHhcC-CCceEeecCCCCCHHHHHHHHHHHhCCC-
Confidence            54  7899999999987665543       56889999999998776543 233443   5899999999999988542 


Q ss_pred             CCCccHHHHHHHHHHHhCCCchHHHHHHHHhccCCHHHHHHHHHHHHhc
Q 039644          141 HPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKREKEVWESAIDKLQRI  189 (192)
Q Consensus       141 ~~~~~~~~~~~~i~~~~~g~Plai~~~~~~l~~~~~~~w~~~l~~l~~~  189 (192)
                        .....+.+.+|++.|+|+||||.++|++|+.. ...|..+++.+.+.
T Consensus       303 --~~~~~~~~~~i~~~~~G~PLal~~~a~~l~~~-~~~w~~~l~~l~~~  348 (591)
T 1z6t_A          303 --KADLPEQAHSIIKECKGSPLVVSLIGALLRDF-PNRWEYYLKQLQNK  348 (591)
T ss_dssp             --GGGSCTHHHHHHHHHTTCHHHHHHHHHHHHHS-TTCHHHHHHHHHSC
T ss_pred             --cccccHHHHHHHHHhCCCcHHHHHHHHHHhcC-chhHHHHHHHHHHh
Confidence              22234567899999999999999999999886 34688888888754

>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=99.16  E-value=5.5e-10  Score=86.90  Aligned_cols=101  Identities=17%  Similarity=0.159  Sum_probs=64.9

Q ss_pred             ceEEEEEeCCCCch-----hHHHhhccCCCCCCCceEEEEecchhHHhh----------c-CC-CceEecCCCCHHHHHH
Q 039644           68 MKVLIVFDDVTCFS-----QLESLMGSLDWLTPVSRIILTTRNKQVLRN----------W-GV-SKIYEMEALEYHHALE  130 (192)
Q Consensus        68 ~~~LlVlDdv~~~~-----~~~~l~~~~~~~~~~~~iivTtR~~~~~~~----------~-~~-~~~~~l~~l~~~ea~~  130 (192)
                      ++.+|||||++...     ++..+...+.....+.++|+|++.......          . +. ...+.+.+|+.+++.+
T Consensus       137 ~~~vlvlDe~~~~~~~~~~~~~~~l~~~~~~~~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~i~l~~l~~~e~~~  216 (357)
T 2fna_A          137 DNVIIVLDEAQELVKLRGVNLLPALAYAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIE  216 (357)
T ss_dssp             SCEEEEEETGGGGGGCTTCCCHHHHHHHHHHCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHH
T ss_pred             CCeEEEEECHHHhhccCchhHHHHHHHHHHcCCCeEEEEEcCchHHHHHHHhccCCCCccccCccceeecCCCCHHHHHH
Confidence            49999999997532     222221111111236789999987653221          1 11 3578999999999999


Q ss_pred             HHHHhhcCCCCCCccHHHHHHHHHHHhCCCchHHHHHHHHhc
Q 039644          131 LFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLH  172 (192)
Q Consensus       131 lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plai~~~~~~l~  172 (192)
                      ++..............    ..+.+.++|+|+++..++..+.
T Consensus       217 ~l~~~~~~~~~~~~~~----~~i~~~t~G~P~~l~~~~~~~~  254 (357)
T 2fna_A          217 FLRRGFQEADIDFKDY----EVVYEKIGGIPGWLTYFGFIYL  254 (357)
T ss_dssp             HHHHHHHHHTCCCCCH----HHHHHHHCSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCcH----HHHHHHhCCCHHHHHHHHHHHc
Confidence            9987542111111111    6899999999999999987654

>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=99.14  E-value=7.8e-10  Score=87.88  Aligned_cols=163  Identities=13%  Similarity=0.114  Sum_probs=98.8

Q ss_pred             CchhHHHHHHHHHhhCC-----Cc-ceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC--c---CchHHHHhhcC--C
Q 039644            1 IGKTAIARAIFDKISGD-----FE-CSCFLENVREESQRPGGLACLRQKLLSNILKDKNV--M---PYIDLNFRRLS--R   67 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~-----F~-~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--~---~~~~~l~~~l~--~   67 (192)
                      +|||+||+.+++.....     |. ..+|+.....     .+...++..++..+....+.  .   +....+...+.  +
T Consensus        63 ~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~  137 (412)
T 1w5s_A           63 IGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNA-----PNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVEN  137 (412)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGC-----CSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHHHhccCCceeEEEEECCCC-----CCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcC
Confidence            69999999999976542     22 2456652222     57778888888888654321  1   13445555553  6


Q ss_pred             ceEEEEEeCCCCc--------hhHHHhhccC---CCCC--CCceEEEEecchhHHhhc---------CCCceEecCCCCH
Q 039644           68 MKVLIVFDDVTCF--------SQLESLMGSL---DWLT--PVSRIILTTRNKQVLRNW---------GVSKIYEMEALEY  125 (192)
Q Consensus        68 ~~~LlVlDdv~~~--------~~~~~l~~~~---~~~~--~~~~iivTtR~~~~~~~~---------~~~~~~~l~~l~~  125 (192)
                      ++++|||||++..        ..+..+...+   +..+  ....+|+||+........         .....+.+++++.
T Consensus       138 ~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~~~~~~~~~~v~lI~~~~~~~~~~~l~~~~~~~~~~~~~~i~l~~l~~  217 (412)
T 1w5s_A          138 HYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKS  217 (412)
T ss_dssp             CEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCH
T ss_pred             CeEEEEEeCHHHHhhccCcchHHHHHHHHHHHhcccCCCCceEEEEEEeccccHHHHHhhhcchhhhhcCCeeeeCCCCH
Confidence            7999999999753        2233332222   1112  344578788765432111         1123399999999


Q ss_pred             HHHHHHHHHhhcCCCCCCccHHHHHHHHHHHhC------CCchHHHHHH
Q 039644          126 HHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQ------GIPLALKVLS  168 (192)
Q Consensus       126 ~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~------g~Plai~~~~  168 (192)
                      +++.++|.........+.....+....+.+.++      |.|..+..+.
T Consensus       218 ~e~~~ll~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~G~p~~~~~l~  266 (412)
T 1w5s_A          218 RELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRAIVAL  266 (412)
T ss_dssp             HHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGTSCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHhccCCCcHHHHHHHH
Confidence            999999976542111111223456778899999      9997555443

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.11  E-value=5.2e-10  Score=86.86  Aligned_cols=162  Identities=18%  Similarity=0.162  Sum_probs=95.5

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccc--cCCCChHHHHHHHHHHHhc----------------CC-----CC-cC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREES--QRPGGLACLRQKLLSNILK----------------DK-----NV-MP   56 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~--~~~~~~~~~~~~l~~~~~~----------------~~-----~~-~~   56 (192)
                      +|||+|+++++++..     .+|++. ....  ..+.....+...+...+..                ..     .. .+
T Consensus        42 ~GKT~Ll~~~~~~~~-----~~~~~~-~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  115 (350)
T 2qen_A           42 VGKSSLLRAFLNERP-----GILIDC-RELYAERGHITREELIKELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLRE  115 (350)
T ss_dssp             SSHHHHHHHHHHHSS-----EEEEEH-HHHHHTTTCBCHHHHHHHHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHH
T ss_pred             CCHHHHHHHHHHHcC-----cEEEEe-ecccccccCCCHHHHHHHHHHHHHHHHhHhhhceeEEEecceeeccccchHHH
Confidence            699999999998752     567662 2211  0112445555555544321                00     01 11


Q ss_pred             chHHHHhhcCC-ceEEEEEeCCCCchh---------HHHhhccCCCCCCCceEEEEecchhHHhh----------c-C-C
Q 039644           57 YIDLNFRRLSR-MKVLIVFDDVTCFSQ---------LESLMGSLDWLTPVSRIILTTRNKQVLRN----------W-G-V  114 (192)
Q Consensus        57 ~~~~l~~~l~~-~~~LlVlDdv~~~~~---------~~~l~~~~~~~~~~~~iivTtR~~~~~~~----------~-~-~  114 (192)
                      ....+...... ++.+|||||++....         +..+...... ..+.++|+|++.......          . + .
T Consensus       116 ~~~~l~~~~~~~~~~vlvlDe~~~~~~~~~~~~~~~~~~L~~~~~~-~~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~  194 (350)
T 2qen_A          116 VFRELNDLGEELGEFIVAFDEAQYLRFYGSRGGKELLALFAYAYDS-LPNLKIILTGSEVGLLHDFLKITDYESPLYGRI  194 (350)
T ss_dssp             HHHHHHHHHHHHSCEEEEEETGGGGGGBTTTTTHHHHHHHHHHHHH-CTTEEEEEEESSHHHHHHHHCTTCTTSTTTTCC
T ss_pred             HHHHHHHHHhccCCEEEEEeCHHHHhccCccchhhHHHHHHHHHHh-cCCeEEEEECCcHHHHHHHHhhcCCCCccccCc
Confidence            33334333332 389999999986432         2222221111 246789999887643211          0 1 1


Q ss_pred             CceEecCCCCHHHHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCCchHHHHHHHHh
Q 039644          115 SKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFL  171 (192)
Q Consensus       115 ~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plai~~~~~~l  171 (192)
                      ...+.+.+|+.+|+.+++..........  ...+.+..+.+.++|+|+++..++..+
T Consensus       195 ~~~i~l~pl~~~e~~~~l~~~~~~~~~~--~~~~~~~~i~~~tgG~P~~l~~~~~~~  249 (350)
T 2qen_A          195 AGEVLVKPFDKDTSVEFLKRGFREVNLD--VPENEIEEAVELLDGIPGWLVVFGVEY  249 (350)
T ss_dssp             CEEEECCCCCHHHHHHHHHHHHHTTTCC--CCHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             cceeeCCCCCHHHHHHHHHHHHHHcCCC--CCHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            3479999999999999998754222211  123567789999999999999988654

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=98.97  E-value=2e-08  Score=73.51  Aligned_cols=102  Identities=13%  Similarity=0.111  Sum_probs=70.4

Q ss_pred             CceEEEEEeCCCCc--hhHHHhhccCCCCCCCceEEEEecchhHHhh--cCCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCF--SQLESLMGSLDWLTPVSRIILTTRNKQVLRN--WGVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~iivTtR~~~~~~~--~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +++.+||+||++..  ..++.+...+.....+..+|+||+.......  ......+.+++++.++..+++...+..... 
T Consensus       125 ~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~~~~~~~l~~r~~~i~l~~l~~~e~~~~l~~~~~~~~~-  203 (250)
T 1njg_A          125 GRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHI-  203 (250)
T ss_dssp             SSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHTTC-
T ss_pred             CCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCChHhCCHHHHHHhhhccCCCCCHHHHHHHHHHHHHhcCC-
Confidence            46799999999753  3455555554444567788888876442211  133468999999999999999877643221 


Q ss_pred             CccHHHHHHHHHHHhCCCchHHHHHHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLALKVLSCF  170 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai~~~~~~  170 (192)
                       ....+....+++.++|.|..+..+...
T Consensus       204 -~~~~~~~~~l~~~~~G~~~~~~~~~~~  230 (250)
T 1njg_A          204 -AHEPRALQLLARAAEGSLRDALSLTDQ  230 (250)
T ss_dssp             -CBCHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             -CCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence             122455778999999999998877653

>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=98.96  E-value=4.2e-08  Score=77.16  Aligned_cols=177  Identities=16%  Similarity=0.124  Sum_probs=104.6

Q ss_pred             CchhHHHHHHHHHhhCC--------CcceEEEeeccccccCCC-ChHHHHHHHHHHHhcCCCC-c-----CchHHHHhhc
Q 039644            1 IGKTAIARAIFDKISGD--------FECSCFLENVREESQRPG-GLACLRQKLLSNILKDKNV-M-----PYIDLNFRRL   65 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~--------F~~~~wv~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~-~-----~~~~~l~~~l   65 (192)
                      +|||+||+.+++.+...        ....+|+.....     . +...++..++..+.+.... .     +....+...+
T Consensus        56 ~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~-----~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l  130 (384)
T 2qby_B           56 TGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREV-----GGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGT  130 (384)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHH-----CSCHHHHHHHHHHHHHCSCCCSSSSCTHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccC-----CCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHh
Confidence            69999999999976433        223455552221     3 6677888888887433222 1     1456667777


Q ss_pred             CCceEEEEEeCCCCchh-------HHHhhccCCCCCCCceEEEEecchhHHhh------cCCCceEecCCCCHHHHHHHH
Q 039644           66 SRMKVLIVFDDVTCFSQ-------LESLMGSLDWLTPVSRIILTTRNKQVLRN------WGVSKIYEMEALEYHHALELF  132 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~~~-------~~~l~~~~~~~~~~~~iivTtR~~~~~~~------~~~~~~~~l~~l~~~ea~~lf  132 (192)
                      ...+.+||||+++....       +..+....    .+..+|+||+.......      ......+.+++++.++..+++
T Consensus       131 ~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~----~~~~iI~~t~~~~~~~~l~~~l~sr~~~~i~l~~l~~~~~~~il  206 (384)
T 2qby_B          131 RNIRAIIYLDEVDTLVKRRGGDIVLYQLLRSD----ANISVIMISNDINVRDYMEPRVLSSLGPSVIFKPYDAEQLKFIL  206 (384)
T ss_dssp             SSSCEEEEEETTHHHHHSTTSHHHHHHHHTSS----SCEEEEEECSSTTTTTTSCHHHHHTCCCEEEECCCCHHHHHHHH
T ss_pred             ccCCCEEEEECHHHhccCCCCceeHHHHhcCC----cceEEEEEECCCchHhhhCHHHHhcCCCeEEECCCCHHHHHHHH
Confidence            76666999999975432       23333222    66788888886531111      111238999999999999999


Q ss_pred             HHhhcCCCCCCccHHHHHHHHHHHhC---CCch-HHHHHHHHh--c-c-C--CHHHHHHHHHHH
Q 039644          133 SQHAFKRNHPDVGYEKLSSNVTKYAQ---GIPL-ALKVLSCFL--H-K-R--EKEVWESAIDKL  186 (192)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~i~~~~~---g~Pl-ai~~~~~~l--~-~-~--~~~~w~~~l~~l  186 (192)
                      ...+........-..+....+++.++   |.|. |+.++-...  . + .  +.+.+..++++.
T Consensus       207 ~~~~~~~~~~~~~~~~~~~~i~~~~~~~~G~~r~a~~~l~~a~~~a~~~~~i~~~~v~~~~~~~  270 (384)
T 2qby_B          207 SKYAEYGLIKGTYDDEILSYIAAISAKEHGDARKAVNLLFRAAQLASGGGIIRKEHVDKAIVDY  270 (384)
T ss_dssp             HHHHHHTSCTTSCCSHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHTTSSSCCCHHHHHHHHHHH
T ss_pred             HHHHHhhcccCCcCHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHH
Confidence            98753111111112234556777777   8877 443333222  1 1 1  266666666554

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=98.79  E-value=1.5e-07  Score=67.96  Aligned_cols=151  Identities=13%  Similarity=0.106  Sum_probs=86.8

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEee-ccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLEN-VREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~-~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~   79 (192)
                      +|||+||+.+++.+........++.. .+.   . .....+. ..+........          ....++.+||+||++.
T Consensus        49 ~GKT~l~~~l~~~~~~~~~~~~~~~~~~~~---~-~~~~~~~-~~~~~~~~~~~----------~~~~~~~vliiDe~~~  113 (226)
T 2chg_A           49 TGKTATAIALARDLFGENWRDNFIEMNASD---E-RGIDVVR-HKIKEFARTAP----------IGGAPFKIIFLDEADA  113 (226)
T ss_dssp             SSHHHHHHHHHHHHHGGGGGGGEEEEETTC---T-TCHHHHH-HHHHHHHTSCC----------STTCSCEEEEEETGGG
T ss_pred             CCHHHHHHHHHHHHhccccccceEEecccc---c-cChHHHH-HHHHHHhcccC----------CCccCceEEEEeChhh
Confidence            69999999999976433322233321 111   0 2222222 22222211100          1135688999999986


Q ss_pred             ch--hHHHhhccCCCCCCCceEEEEecchhHHhh--cCCCceEecCCCCHHHHHHHHHHhhcCCCCCCccHHHHHHHHHH
Q 039644           80 FS--QLESLMGSLDWLTPVSRIILTTRNKQVLRN--WGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTK  155 (192)
Q Consensus        80 ~~--~~~~l~~~~~~~~~~~~iivTtR~~~~~~~--~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~  155 (192)
                      ..  ..+.+...+.....++.+|+||+.......  ......+.+.+++.++..+++...+.....  ....+....+++
T Consensus       114 l~~~~~~~l~~~l~~~~~~~~~i~~~~~~~~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~--~~~~~~~~~l~~  191 (226)
T 2chg_A          114 LTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGV--KITEDGLEALIY  191 (226)
T ss_dssp             SCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTC--CBCHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcCHHHHHhCceeecCCCCHHHHHHHHHHHHHHcCC--CCCHHHHHHHHH
Confidence            42  344444444334556788888876532111  123347999999999999998876632111  122455677889


Q ss_pred             HhCCCchHHHHHH
Q 039644          156 YAQGIPLALKVLS  168 (192)
Q Consensus       156 ~~~g~Plai~~~~  168 (192)
                      .++|.|..+..+.
T Consensus       192 ~~~g~~r~l~~~l  204 (226)
T 2chg_A          192 ISGGDFRKAINAL  204 (226)
T ss_dssp             HHTTCHHHHHHHH
T ss_pred             HcCCCHHHHHHHH
Confidence            9999999654443

>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=98.70  E-value=6.4e-08  Score=75.90  Aligned_cols=159  Identities=14%  Similarity=0.121  Sum_probs=90.8

Q ss_pred             CchhHHHHHHHHHhhCCC---cceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC--cC---chHHHHhhcC--CceE
Q 039644            1 IGKTAIARAIFDKISGDF---ECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV--MP---YIDLNFRRLS--RMKV   70 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F---~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--~~---~~~~l~~~l~--~~~~   70 (192)
                      +||||||+.+++.+...+   ...+|+.....     .....+...++..+....+.  ..   ....+...+.  +++.
T Consensus        56 ~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~~-----~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~  130 (386)
T 2qby_A           56 TGKTAVVKFVLSKLHKKFLGKFKHVYINTRQI-----DTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQV  130 (386)
T ss_dssp             SSHHHHHHHHHHHHHHHTCSSCEEEEEEHHHH-----CSHHHHHHHHTTTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCE
T ss_pred             CCHHHHHHHHHHHHHHHhcCCceEEEEECCCC-----CCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeE
Confidence            699999999999876543   23456652221     35566666766665432211  11   3344444443  4589


Q ss_pred             EEEEeCCCCc------hhHHHhhccCCC-CCCCceEEEEecchhHHhhc------C-CCceEecCCCCHHHHHHHHHHhh
Q 039644           71 LIVFDDVTCF------SQLESLMGSLDW-LTPVSRIILTTRNKQVLRNW------G-VSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus        71 LlVlDdv~~~------~~~~~l~~~~~~-~~~~~~iivTtR~~~~~~~~------~-~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      +||||+++..      ..+..+...+.. ...+..+|++|+........      . ....+.+++++.++..+++...+
T Consensus       131 vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~~~~~~~~~~~~~~~~~r~~~~~i~l~~l~~~~~~~il~~~~  210 (386)
T 2qby_A          131 VIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITNDVKFVDLLDPRVKSSLSEEEIIFPPYNAEELEDILTKRA  210 (386)
T ss_dssp             EEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEEEESCGGGGGGCTTHHHHTTTTEEEEECCCCHHHHHHHHHHHH
T ss_pred             EEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEEEECCCChHhhhCHHHhccCCCeeEEeCCCCHHHHHHHHHHHH
Confidence            9999999753      223333322211 13455678888765432221      1 12579999999999999998754


Q ss_pred             cCCCCCCccHHHHHHHHHHHhC---CCchHH
Q 039644          137 FKRNHPDVGYEKLSSNVTKYAQ---GIPLAL  164 (192)
Q Consensus       137 ~~~~~~~~~~~~~~~~i~~~~~---g~Plai  164 (192)
                      ...........+....+.+.++   |.|..+
T Consensus       211 ~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~  241 (386)
T 2qby_A          211 QMAFKPGVLPDNVIKLCAALAAREHGDARRA  241 (386)
T ss_dssp             HHHBCSSCSCHHHHHHHHHHHHHTTCCHHHH
T ss_pred             HhhccCCCCCHHHHHHHHHHHHHhcCCHHHH
Confidence            2111111222344556666666   998843

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=98.69  E-value=1.8e-07  Score=73.45  Aligned_cols=157  Identities=13%  Similarity=0.118  Sum_probs=90.7

Q ss_pred             CchhHHHHHHHHHhhCCC------cceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC--cC---chHHHHhhc--CC
Q 039644            1 IGKTAIARAIFDKISGDF------ECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV--MP---YIDLNFRRL--SR   67 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F------~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--~~---~~~~l~~~l--~~   67 (192)
                      +|||+||+.+++.....+      ...+|+.....     .+...++..++..+....+.  ..   ....+...+  .+
T Consensus        55 ~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~-----~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~  129 (387)
T 2v1u_A           55 TGKTAVARLVLRRLEARASSLGVLVKPIYVNARHR-----ETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLR  129 (387)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTTS-----CSHHHHHHHHHHHHSCCCCSSCCCHHHHHHHHHHHHTTSC
T ss_pred             CCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCcC-----CCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccC
Confidence            699999999999764321      23455552221     56778888888888553322  11   344555555  34


Q ss_pred             ceEEEEEeCCCCchh-------HHHhhccCCCC--CCCceEEEEecchhHHhhc-----C-C-CceEecCCCCHHHHHHH
Q 039644           68 MKVLIVFDDVTCFSQ-------LESLMGSLDWL--TPVSRIILTTRNKQVLRNW-----G-V-SKIYEMEALEYHHALEL  131 (192)
Q Consensus        68 ~~~LlVlDdv~~~~~-------~~~l~~~~~~~--~~~~~iivTtR~~~~~~~~-----~-~-~~~~~l~~l~~~ea~~l  131 (192)
                      ++.+|+||+++....       +..+.......  ..+..+|.+|+........     . . ...+.+++++.++..++
T Consensus       130 ~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~I~~t~~~~~~~~l~~~l~~r~~~~~i~l~~l~~~~~~~i  209 (387)
T 2v1u_A          130 GIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKSSLGEVELVFPPYTAPQLRDI  209 (387)
T ss_dssp             SEEEEEEETTTHHHHSTTHHHHHHHHHHGGGCC-----CEEEEECSCSTTSSSSCHHHHTTTTSEECCBCCCCHHHHHHH
T ss_pred             CeEEEEEccHhhhcccCCCChHHHhHhhchhhcCCCceEEEEEEECCCchHhhhCHHHHhcCCCeEEeeCCCCHHHHHHH
Confidence            689999999985431       22222222211  3456777777765221111     1 1 24789999999999999


Q ss_pred             HHHhhcCCCCCCccHHHHHHHHHHHhC---CCch
Q 039644          132 FSQHAFKRNHPDVGYEKLSSNVTKYAQ---GIPL  162 (192)
Q Consensus       132 f~~~~~~~~~~~~~~~~~~~~i~~~~~---g~Pl  162 (192)
                      +...+...........+....+.+.++   |.|.
T Consensus       210 l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r  243 (387)
T 2v1u_A          210 LETRAEEAFNPGVLDPDVVPLCAALAAREHGDAR  243 (387)
T ss_dssp             HHHHHHHHBCTTTBCSSHHHHHHHHHHSSSCCHH
T ss_pred             HHHHHHhhccCCCCCHHHHHHHHHHHHHhccCHH
Confidence            987753200011111233456777777   9994

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=98.66  E-value=6.9e-07  Score=70.21  Aligned_cols=162  Identities=10%  Similarity=0.120  Sum_probs=98.5

Q ss_pred             CchhHHHHHHHHHhhCCC-cceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC--cC---chHHHHhhc--CCceEEE
Q 039644            1 IGKTAIARAIFDKISGDF-ECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV--MP---YIDLNFRRL--SRMKVLI   72 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F-~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--~~---~~~~l~~~l--~~~~~Ll   72 (192)
                      +|||||++.++....... ...+++.. ...    .+...+...++..+....+.  ..   ....+...+  .+++.+|
T Consensus        55 ~GKTtl~~~l~~~~~~~~~~~~~~i~~-~~~----~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vl  129 (389)
T 1fnn_A           55 TGKTVTLRKLWELYKDKTTARFVYING-FIY----RNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFL  129 (389)
T ss_dssp             SSHHHHHHHHHHHHTTSCCCEEEEEET-TTC----CSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEE
T ss_pred             CCHHHHHHHHHHHHhhhcCeeEEEEeC-ccC----CCHHHHHHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEE
Confidence            699999999999876542 23455552 221    45677888888777543222  11   333444444  3568999


Q ss_pred             EEeCCCCc--hhHHHhhccCCCCC----CCceEEEEecchhHHhhcC-------CCceEecCCCCHHHHHHHHHHhhcCC
Q 039644           73 VFDDVTCF--SQLESLMGSLDWLT----PVSRIILTTRNKQVLRNWG-------VSKIYEMEALEYHHALELFSQHAFKR  139 (192)
Q Consensus        73 VlDdv~~~--~~~~~l~~~~~~~~----~~~~iivTtR~~~~~~~~~-------~~~~~~l~~l~~~ea~~lf~~~~~~~  139 (192)
                      +||+++..  .....+...+....    .+..+|++|+.........       ....+.+++++.++..+++...+...
T Consensus       130 ilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~~~~~l~~~~~~r~~~~~i~~~pl~~~~~~~~l~~~~~~~  209 (389)
T 1fnn_A          130 VLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAG  209 (389)
T ss_dssp             EEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHH
T ss_pred             EEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEECCchHHHHhCHHhhhcCCCceEEeCCCCHHHHHHHHHHHHHhh
Confidence            99999864  33455544443211    3667888887654332221       12369999999999999998765321


Q ss_pred             CCCCccHHHHHHHHHHHh---------CCCchHHHHH
Q 039644          140 NHPDVGYEKLSSNVTKYA---------QGIPLALKVL  167 (192)
Q Consensus       140 ~~~~~~~~~~~~~i~~~~---------~g~Plai~~~  167 (192)
                      .....-..+....+.+.+         .|.|..+..+
T Consensus       210 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~  246 (389)
T 1fnn_A          210 LAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDI  246 (389)
T ss_dssp             BCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHHhhcccCCCCCCcHHHHHHH
Confidence            111122345677788888         7887544433

>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=98.46  E-value=1.7e-06  Score=66.30  Aligned_cols=151  Identities=13%  Similarity=0.175  Sum_probs=87.0

Q ss_pred             CchhHHHHHHHHHhhCC-Cc-ceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhc-CCceEEEEEeCC
Q 039644            1 IGKTAIARAIFDKISGD-FE-CSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRL-SRMKVLIVFDDV   77 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~-F~-~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l-~~~~~LlVlDdv   77 (192)
                      +|||++|+.+++.+... +. ..+++. .+.   . .... ....++..+.....          .+ .+++.++|+|++
T Consensus        53 ~GKt~la~~l~~~l~~~~~~~~~~~~~-~~~---~-~~~~-~i~~~~~~~~~~~~----------~~~~~~~~viiiDe~  116 (323)
T 1sxj_B           53 IGKTTSVHCLAHELLGRSYADGVLELN-ASD---D-RGID-VVRNQIKHFAQKKL----------HLPPGKHKIVILDEA  116 (323)
T ss_dssp             SSHHHHHHHHHHHHHGGGHHHHEEEEC-TTS---C-CSHH-HHHTHHHHHHHBCC----------CCCTTCCEEEEEESG
T ss_pred             CCHHHHHHHHHHHhcCCcccCCEEEec-Ccc---c-cChH-HHHHHHHHHHhccc----------cCCCCCceEEEEECc
Confidence            69999999999986332 22 223333 211   0 1222 22233333321100          12 345889999999


Q ss_pred             CCch--hHHHhhccCCCCCCCceEEEEecchhHHh-h-cCCCceEecCCCCHHHHHHHHHHhhcCCCCCCccHHHHHHHH
Q 039644           78 TCFS--QLESLMGSLDWLTPVSRIILTTRNKQVLR-N-WGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNV  153 (192)
Q Consensus        78 ~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~~~~-~-~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i  153 (192)
                      +...  ..+.+...+.....++.+|++|+...... . .+....+.+.+++.++..+++...+.....  ....+....+
T Consensus       117 ~~l~~~~~~~L~~~le~~~~~~~~il~~~~~~~l~~~l~sr~~~i~~~~~~~~~~~~~l~~~~~~~~~--~~~~~~~~~l  194 (323)
T 1sxj_B          117 DSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDV--KYTNDGLEAI  194 (323)
T ss_dssp             GGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTC--CBCHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHhccCCCceEEEEeCChhhchhHHHhhceEEeecCCCHHHHHHHHHHHHHHcCC--CCCHHHHHHH
Confidence            8643  34444444333345678888887643211 1 134468999999999999999876532111  1224556788


Q ss_pred             HHHhCCCch-HHHHHHH
Q 039644          154 TKYAQGIPL-ALKVLSC  169 (192)
Q Consensus       154 ~~~~~g~Pl-ai~~~~~  169 (192)
                      ++.++|.|. |+..+..
T Consensus       195 ~~~~~G~~r~a~~~l~~  211 (323)
T 1sxj_B          195 IFTAEGDMRQAINNLQS  211 (323)
T ss_dssp             HHHHTTCHHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHHH
Confidence            999999995 4454443

>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=98.23  E-value=8.2e-06  Score=62.51  Aligned_cols=99  Identities=12%  Similarity=0.081  Sum_probs=64.4

Q ss_pred             CceEEEEEeCCCCc--hhHHHhhccCCCCCCCceEEEEecchhHHhh--cCCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCF--SQLESLMGSLDWLTPVSRIILTTRNKQVLRN--WGVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~iivTtR~~~~~~~--~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +++.++|+|+++..  ...+.+...+.....++++|+||........  ......+.+.+++.++...++...+....  
T Consensus       109 ~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~~~~~~l~~~~~~~~l~~~~~~~~--  186 (327)
T 1iqp_A          109 ASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEG--  186 (327)
T ss_dssp             CSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEECCCCCHHHHHHHHHHHHHTTT--
T ss_pred             CCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCccccCHHHHhhCcEEEecCCCHHHHHHHHHHHHHhcC--
Confidence            56789999999864  3345554444434556788888876432111  12234789999999999998887664322  


Q ss_pred             CccHHHHHHHHHHHhCCCchHHHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLALKVL  167 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai~~~  167 (192)
                      ..-..+....+++.++|.|..+..+
T Consensus       187 ~~~~~~~~~~l~~~~~g~~r~~~~~  211 (327)
T 1iqp_A          187 LELTEEGLQAILYIAEGDMRRAINI  211 (327)
T ss_dssp             CEECHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CCCCHHHHHHHHHHCCCCHHHHHHH
Confidence            1223456677888899998865443

>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=98.22  E-value=7.4e-06  Score=65.92  Aligned_cols=149  Identities=9%  Similarity=0.079  Sum_probs=84.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +||||||+.+++.+...|+..-++.         .+..++...+...+...     ....+...+...+.+|+||+++..
T Consensus       141 ~GKTtLa~aia~~l~~~~~~~~v~~---------v~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~vL~IDEi~~l  206 (440)
T 2z4s_A          141 LGKTHLLQSIGNYVVQNEPDLRVMY---------ITSEKFLNDLVDSMKEG-----KLNEFREKYRKKVDILLIDDVQFL  206 (440)
T ss_dssp             SSHHHHHHHHHHHHHHHCCSSCEEE---------EEHHHHHHHHHHHHHTT-----CHHHHHHHHTTTCSEEEEECGGGG
T ss_pred             CCHHHHHHHHHHHHHHhCCCCeEEE---------eeHHHHHHHHHHHHHcc-----cHHHHHHHhcCCCCEEEEeCcccc
Confidence            6999999999998766554332222         12233444444444332     223344444546779999999743


Q ss_pred             h----hHHHhhccCCC-CCCCceEEEEecchh---------HHhhcCCCceEecCCCCHHHHHHHHHHhhcCCCCCCccH
Q 039644           81 S----QLESLMGSLDW-LTPVSRIILTTRNKQ---------VLRNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGY  146 (192)
Q Consensus        81 ~----~~~~l~~~~~~-~~~~~~iivTtR~~~---------~~~~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~  146 (192)
                      .    ..+.+...+.. ...|..||+||....         +...+.....+.+++++.++..+++...+.....  ...
T Consensus       207 ~~~~~~q~~l~~~l~~l~~~~~~iIitt~~~~~~l~~l~~~L~sR~~~g~~i~l~~p~~e~r~~iL~~~~~~~~~--~i~  284 (440)
T 2z4s_A          207 IGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKSIARKMLEIEHG--ELP  284 (440)
T ss_dssp             SSCHHHHHHHHHHHHHHHTTTCEEEEEESSCGGGCSSCCHHHHHHHHSSBCCBCCCCCHHHHHHHHHHHHHHHTC--CCC
T ss_pred             cCChHHHHHHHHHHHHHHHCCCeEEEEECCCHHHHHHHHHHHHhhccCCeEEEeCCCCHHHHHHHHHHHHHHcCC--CCC
Confidence            2    12223222211 134667888887632         2222333457889999999999998876532111  011


Q ss_pred             HHHHHHHHHHhCCCchHHH
Q 039644          147 EKLSSNVTKYAQGIPLALK  165 (192)
Q Consensus       147 ~~~~~~i~~~~~g~Plai~  165 (192)
                      .+....|++.+.|.+..+.
T Consensus       285 ~e~l~~la~~~~gn~R~l~  303 (440)
T 2z4s_A          285 EEVLNFVAENVDDNLRRLR  303 (440)
T ss_dssp             TTHHHHHHHHCCSCHHHHH
T ss_pred             HHHHHHHHHhcCCCHHHHH
Confidence            1234566677777776443

>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=98.08  E-value=5e-05  Score=59.24  Aligned_cols=100  Identities=13%  Similarity=0.127  Sum_probs=64.5

Q ss_pred             CceEEEEEeCCCCc--hhHHHhhccCCCCCCCceEEEEecchhHH-h-hcCCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCF--SQLESLMGSLDWLTPVSRIILTTRNKQVL-R-NWGVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~iivTtR~~~~~-~-~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +++.++|+|+++..  ...+.+...+.....+..+|++|...... . .......+.+.+++.++..+++...+..... 
T Consensus       118 ~~~~vliiDe~~~l~~~~~~~Ll~~le~~~~~~~~Il~~~~~~~l~~~l~sr~~~i~~~~l~~~~~~~~l~~~~~~~~~-  196 (373)
T 1jr3_A          118 GRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHI-  196 (373)
T ss_dssp             SSSEEEEEECGGGSCHHHHHHHHHHHHSCCSSEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTC-
T ss_pred             CCeEEEEEECcchhcHHHHHHHHHHHhcCCCceEEEEEeCChHhCcHHHHhheeEeeCCCCCHHHHHHHHHHHHHHcCC-
Confidence            45789999999754  33555555444444566777777654321 1 1134578999999999999988876522111 


Q ss_pred             CccHHHHHHHHHHHhCCCchHHHHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLALKVLS  168 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai~~~~  168 (192)
                       ....+....+++.++|.|..+..+.
T Consensus       197 -~~~~~a~~~l~~~~~G~~r~~~~~l  221 (373)
T 1jr3_A          197 -AHEPRALQLLARAAEGSLRDALSLT  221 (373)
T ss_dssp             -CBCHHHHHHHHHHSSSCHHHHHHHH
T ss_pred             -CCCHHHHHHHHHHCCCCHHHHHHHH
Confidence             1123456678889999998776544

>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=98.05  E-value=0.00014  Score=55.28  Aligned_cols=98  Identities=9%  Similarity=0.028  Sum_probs=64.7

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchhHHh-h-cCCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQVLR-N-WGVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~~~~-~-~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +++.++|+|+++...  ..+.+...+.....++.+|++|....... . ......+.+.+++.++..+++...+..... 
T Consensus       101 ~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~i~~~~~~~~~~~~~l~~~~~~~~~-  179 (319)
T 2chq_A          101 APFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGV-  179 (319)
T ss_dssp             CCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCGGGSCHHHHTTCEEEECCCCCHHHHHHHHHHHHHTTCC-
T ss_pred             CCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcchHHHhhCeEEEecCCCHHHHHHHHHHHHHHcCC-
Confidence            567899999998643  35566666655556778888886644111 1 133458999999999999988876643221 


Q ss_pred             CccHHHHHHHHHHHhCCCchHHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLALKV  166 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai~~  166 (192)
                       .-..+....+++.++|.+..+..
T Consensus       180 -~i~~~~l~~l~~~~~G~~r~~~~  202 (319)
T 2chq_A          180 -KITEDGLEALIYISGGDFRKAIN  202 (319)
T ss_dssp             -CBCHHHHHHHHHTTTTCHHHHHH
T ss_pred             -CCCHHHHHHHHHHcCCCHHHHHH
Confidence             12344566777888888875443

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=98.01  E-value=0.00019  Score=55.53  Aligned_cols=94  Identities=14%  Similarity=0.147  Sum_probs=63.7

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +++-++|+|+++...  ..+.+...+.....++.+|++|.+.. +.... +....+.+++++.++..+.+....   .  
T Consensus       107 ~~~kvviIdead~l~~~a~naLLk~lEep~~~~~~Il~t~~~~~l~~ti~SRc~~~~~~~~~~~~~~~~L~~~~---~--  181 (334)
T 1a5t_A          107 GGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREV---T--  181 (334)
T ss_dssp             SSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHC---C--
T ss_pred             CCcEEEEECchhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHhhcceeeeCCCCCHHHHHHHHHHhc---C--
Confidence            457799999998653  35566655555456777888877653 11111 455789999999999999887764   1  


Q ss_pred             CccHHHHHHHHHHHhCCCchHHHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLALKVL  167 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai~~~  167 (192)
                        ...+....+++.++|.|..+..+
T Consensus       182 --~~~~~~~~l~~~s~G~~r~a~~~  204 (334)
T 1a5t_A          182 --MSQDALLAALRLSAGSPGAALAL  204 (334)
T ss_dssp             --CCHHHHHHHHHHTTTCHHHHHHT
T ss_pred             --CCHHHHHHHHHHcCCCHHHHHHH
Confidence              12344567888899998765443

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=97.98  E-value=2e-05  Score=57.57  Aligned_cols=139  Identities=13%  Similarity=0.116  Sum_probs=77.8

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||+||+.+++........+.|+. .+.....   ..                 +..    ..+ .++.+||||+++..
T Consensus        63 ~GKT~la~~l~~~~~~~~~~~~~~~-~~~~~~~---~~-----------------~~~----~~~-~~~~vliiDe~~~~  116 (242)
T 3bos_A           63 SGRTHLIHAACARANELERRSFYIP-LGIHASI---ST-----------------ALL----EGL-EQFDLICIDDVDAV  116 (242)
T ss_dssp             SSHHHHHHHHHHHHHHTTCCEEEEE-GGGGGGS---CG-----------------GGG----TTG-GGSSEEEEETGGGG
T ss_pred             CCHHHHHHHHHHHHHHcCCeEEEEE-HHHHHHH---HH-----------------HHH----Hhc-cCCCEEEEeccccc
Confidence            6999999999997655444456665 2221100   00                 000    011 34569999999754


Q ss_pred             hh----HHHhhccCCCC-CCCc-eEEEEecchh---------HHhhcCCCceEecCCCCHHHHHHHHHHhhcCCCCCCcc
Q 039644           81 SQ----LESLMGSLDWL-TPVS-RIILTTRNKQ---------VLRNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVG  145 (192)
Q Consensus        81 ~~----~~~l~~~~~~~-~~~~-~iivTtR~~~---------~~~~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~  145 (192)
                      ..    .+.+...+... ..+. ++|+||+...         +...+.....+.+++++.++..+++...+.....  ..
T Consensus       117 ~~~~~~~~~l~~~l~~~~~~~~~~ii~~~~~~~~~~~~~~~~l~~r~~~~~~i~l~~~~~~~~~~~l~~~~~~~~~--~~  194 (242)
T 3bos_A          117 AGHPLWEEAIFDLYNRVAEQKRGSLIVSASASPMEAGFVLPDLVSRMHWGLTYQLQPMMDDEKLAALQRRAAMRGL--QL  194 (242)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHCSCEEEEEESSCTTTTTCCCHHHHHHHHHSEEEECCCCCGGGHHHHHHHHHHHTTC--CC
T ss_pred             cCCHHHHHHHHHHHHHHHHcCCCeEEEEcCCCHHHHHHhhhhhhhHhhcCceEEeCCCCHHHHHHHHHHHHHHcCC--CC
Confidence            21    22222221110 1122 4788876432         1111112367999999999999998876632211  12


Q ss_pred             HHHHHHHHHHHhCCCchHHHHH
Q 039644          146 YEKLSSNVTKYAQGIPLALKVL  167 (192)
Q Consensus       146 ~~~~~~~i~~~~~g~Plai~~~  167 (192)
                      ..+....+++.++|.+..+..+
T Consensus       195 ~~~~~~~l~~~~~g~~r~l~~~  216 (242)
T 3bos_A          195 PEDVGRFLLNRMARDLRTLFDV  216 (242)
T ss_dssp             CHHHHHHHHHHTTTCHHHHHHH
T ss_pred             CHHHHHHHHHHccCCHHHHHHH
Confidence            3455677888899988766544

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=97.91  E-value=0.00046  Score=51.59  Aligned_cols=118  Identities=19%  Similarity=0.140  Sum_probs=64.6

Q ss_pred             CCceEEEEEeCCCCc-----------h-hHHHhhccCCC---CCCCceEEEEecchhHHhh---c-CCCceEecCCCCH-
Q 039644           66 SRMKVLIVFDDVTCF-----------S-QLESLMGSLDW---LTPVSRIILTTRNKQVLRN---W-GVSKIYEMEALEY-  125 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~-----------~-~~~~l~~~~~~---~~~~~~iivTtR~~~~~~~---~-~~~~~~~l~~l~~-  125 (192)
                      ...+.+|+||+++..           . ..+.+...+..   .+....||.||........   . .....+.+++++. 
T Consensus       122 ~~~~~vl~iDEid~l~~~~~~~~~~~~~~l~~L~~~~~~~~~~~~~~~ii~ttn~~~~l~~~~l~~rf~~~i~~p~l~~r  201 (272)
T 1d2n_A          122 KSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEMLNAFSTTIHVPNIATG  201 (272)
T ss_dssp             TSSEEEEEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTCEEEEEEEESCHHHHHHTTCTTTSSEEEECCCEEEH
T ss_pred             hcCCcEEEEEChhhhhccCCCChhHHHHHHHHHHHHhcCccCCCCCEEEEEecCChhhcchhhhhcccceEEcCCCccHH
Confidence            456889999998643           1 12333222221   2233446667776644332   1 2246788998887 


Q ss_pred             HHHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCC------chHHHHHHHHhccCCHHHHHHHHHHHHhcC
Q 039644          126 HHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGI------PLALKVLSCFLHKREKEVWESAIDKLQRIL  190 (192)
Q Consensus       126 ~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~------Plai~~~~~~l~~~~~~~w~~~l~~l~~~~  190 (192)
                      ++...++....   .    ...+....+++.+.|.      .-++.++-..........++.+++.+++..
T Consensus       202 ~~i~~i~~~~~---~----~~~~~~~~l~~~~~g~~~~g~ir~l~~~l~~a~~~~~~~~~~~~~~~l~~~~  265 (272)
T 1d2n_A          202 EQLLEALELLG---N----FKDKERTTIAQQVKGKKVWIGIKKLLMLIEMSLQMDPEYRVRKFLALLREEG  265 (272)
T ss_dssp             HHHHHHHHHHT---C----SCHHHHHHHHHHHTTSEEEECHHHHHHHHHHHTTSCGGGHHHHHHHHHHHTS
T ss_pred             HHHHHHHHhcC---C----CCHHHHHHHHHHhcCCCccccHHHHHHHHHHHhhhchHHHHHHHHHHHHHcC
Confidence            55556555431   1    1234566788888884      333333333322223667778887777553

>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=97.71  E-value=0.00031  Score=53.67  Aligned_cols=142  Identities=13%  Similarity=0.066  Sum_probs=79.5

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||+||+.+++.....|   .++. ....    ....++..    .+..             . ...+.+|+||+++..
T Consensus        49 tGKT~la~~i~~~~~~~~---~~~~-~~~~----~~~~~l~~----~l~~-------------~-~~~~~~l~lDEi~~l  102 (324)
T 1hqc_A           49 LGKTTLAHVIAHELGVNL---RVTS-GPAI----EKPGDLAA----ILAN-------------S-LEEGDILFIDEIHRL  102 (324)
T ss_dssp             CCCHHHHHHHHHHHTCCE---EEEC-TTTC----CSHHHHHH----HHTT-------------T-CCTTCEEEETTTTSC
T ss_pred             CCHHHHHHHHHHHhCCCE---EEEe-cccc----CChHHHHH----HHHH-------------h-ccCCCEEEEECCccc
Confidence            699999999999774332   2333 2111    12222221    1111             0 124568999999865


Q ss_pred             h--hHHHhhccCCCC------------------CCCceEEEEecchhHHhh-c--CCCceEecCCCCHHHHHHHHHHhhc
Q 039644           81 S--QLESLMGSLDWL------------------TPVSRIILTTRNKQVLRN-W--GVSKIYEMEALEYHHALELFSQHAF  137 (192)
Q Consensus        81 ~--~~~~l~~~~~~~------------------~~~~~iivTtR~~~~~~~-~--~~~~~~~l~~l~~~ea~~lf~~~~~  137 (192)
                      .  ....+...+...                  .++..+|.+|........ .  .....+.+.+++.++...++...+.
T Consensus       103 ~~~~~~~L~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~~i~~t~~~~~~~~~l~~R~~~~i~l~~~~~~e~~~~l~~~~~  182 (324)
T 1hqc_A          103 SRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDAR  182 (324)
T ss_dssp             CHHHHHHHHHHHHHSEEEECCSSSSSCCCEEEECCCCEEEEEESCCSSCSCSTTTTCSCEEECCCCCHHHHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHhhhhHHhccccccccccccCCCCEEEEEeCCCcccCCHHHHhcccEEEecCCCCHHHHHHHHHHHHH
Confidence            3  222222111100                  023557766664332111 1  1235789999999999999887764


Q ss_pred             CCCCCCccHHHHHHHHHHHhCCCchHHHHHHHH
Q 039644          138 KRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCF  170 (192)
Q Consensus       138 ~~~~~~~~~~~~~~~i~~~~~g~Plai~~~~~~  170 (192)
                      ....  .-..+....+++.+.|.|..+..+...
T Consensus       183 ~~~~--~~~~~~~~~l~~~~~G~~r~l~~~l~~  213 (324)
T 1hqc_A          183 LLGV--RITEEAALEIGRRSRGTMRVAKRLFRR  213 (324)
T ss_dssp             TTTC--CCCHHHHHHHHHHSCSCHHHHHHHHHH
T ss_pred             hcCC--CCCHHHHHHHHHHccCCHHHHHHHHHH
Confidence            3221  123456778889999999887766543

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.65  E-value=0.00077  Score=52.03  Aligned_cols=98  Identities=11%  Similarity=0.118  Sum_probs=60.5

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchhHH-hhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQVL-RNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~~~-~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      ..+-++++|+++...  ....+...+.......++|++|...... ... .....+.+.+++.++....+...+..... 
T Consensus       132 ~~~~vliiDE~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~~~~~~~-  210 (353)
T 1sxj_D          132 PPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFISEQENV-  210 (353)
T ss_dssp             CSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEEECCCCCHHHHHHHHHHHHHTTTC-
T ss_pred             CCceEEEEECCCccCHHHHHHHHHHHHhcCCCceEEEEeCchhhCcchhhccCceEEeCCCCHHHHHHHHHHHHHHhCC-
Confidence            355799999997542  2344444333334456788877554311 111 22357899999999999988876533221 


Q ss_pred             CccHHHHHHHHHHHhCCCchHHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLALKV  166 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai~~  166 (192)
                       .-..+....+++.++|.|..+..
T Consensus       211 -~i~~~~l~~l~~~~~G~~r~~~~  233 (353)
T 1sxj_D          211 -KCDDGVLERILDISAGDLRRGIT  233 (353)
T ss_dssp             -CCCHHHHHHHHHHTSSCHHHHHH
T ss_pred             -CCCHHHHHHHHHHcCCCHHHHHH
Confidence             12245667888899999886443

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=97.60  E-value=0.0011  Score=50.87  Aligned_cols=141  Identities=13%  Similarity=0.095  Sum_probs=75.4

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||+||+.+++.....-...+++.           ..++...+...+...     ....+...+. ++.+|+||+++..
T Consensus        48 tGKT~la~~i~~~~~~~~~~~~~i~-----------~~~~~~~~~~~~~~~-----~~~~~~~~~~-~~~vL~iDEi~~l  110 (324)
T 1l8q_A           48 TGKTHLLQAAGNEAKKRGYRVIYSS-----------ADDFAQAMVEHLKKG-----TINEFRNMYK-SVDLLLLDDVQFL  110 (324)
T ss_dssp             SSHHHHHHHHHHHHHHTTCCEEEEE-----------HHHHHHHHHHHHHHT-----CHHHHHHHHH-TCSEEEEECGGGG
T ss_pred             CcHHHHHHHHHHHHHHCCCEEEEEE-----------HHHHHHHHHHHHHcC-----cHHHHHHHhc-CCCEEEEcCcccc
Confidence            6999999999997643312234443           223333333333221     1222222222 3669999999754


Q ss_pred             h---h-HHHhhccCCC-CCCCceEEEEecchh---------HHhhcCCCceEecCCCCHHHHHHHHHHhhcCCCCCCccH
Q 039644           81 S---Q-LESLMGSLDW-LTPVSRIILTTRNKQ---------VLRNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGY  146 (192)
Q Consensus        81 ~---~-~~~l~~~~~~-~~~~~~iivTtR~~~---------~~~~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~  146 (192)
                      .   . .+.+...+.. ...+..+|+||....         +...+.....+.+++ +.++..+++...+.....  .-.
T Consensus       111 ~~~~~~~~~l~~~l~~~~~~~~~iii~~~~~~~~l~~l~~~L~sR~~~~~~i~l~~-~~~e~~~il~~~~~~~~~--~l~  187 (324)
T 1l8q_A          111 SGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIEL-DNKTRFKIIKEKLKEFNL--ELR  187 (324)
T ss_dssp             TTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECCC-CHHHHHHHHHHHHHHTTC--CCC
T ss_pred             cCChHHHHHHHHHHHHHHHCCCeEEEEecCChHHHHHhhhHhhhcccCceEEEeCC-CHHHHHHHHHHHHHhcCC--CCC
Confidence            3   1 1222222111 124557888876432         222222335789999 999999998877642221  112


Q ss_pred             HHHHHHHHHHhCCCch
Q 039644          147 EKLSSNVTKYAQGIPL  162 (192)
Q Consensus       147 ~~~~~~i~~~~~g~Pl  162 (192)
                      .+....+.+.+ |.+-
T Consensus       188 ~~~l~~l~~~~-g~~r  202 (324)
T 1l8q_A          188 KEVIDYLLENT-KNVR  202 (324)
T ss_dssp             HHHHHHHHHHC-SSHH
T ss_pred             HHHHHHHHHhC-CCHH
Confidence            34455667777 6654

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=97.59  E-value=0.0015  Score=49.02  Aligned_cols=118  Identities=22%  Similarity=0.322  Sum_probs=63.3

Q ss_pred             CCceEEEEEeCCCCc-----------h-----hHHHhhccCC--CCCCCceEEEEecchhHHhh-----cCCCceEecCC
Q 039644           66 SRMKVLIVFDDVTCF-----------S-----QLESLMGSLD--WLTPVSRIILTTRNKQVLRN-----WGVSKIYEMEA  122 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~-----------~-----~~~~l~~~~~--~~~~~~~iivTtR~~~~~~~-----~~~~~~~~l~~  122 (192)
                      ...+.+|+||+++..           .     .+..+...+.  ....+..||.||........     ......+.++.
T Consensus       108 ~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~  187 (285)
T 3h4m_A          108 EKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPA  187 (285)
T ss_dssp             HTCSEEEEEETTHHHHBCCSSSCCGGGGHHHHHHHHHHHHHHTTCSSSSEEEEEECSCGGGBCHHHHSTTSEEEEEECCC
T ss_pred             HcCCeEEEEECHHHhcccCccccCCccHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCchhcCHHHcCCCcCCeEEEECC
Confidence            345689999999643           1     1222222221  12235567777765432211     12234788999


Q ss_pred             CCHHHHHHHHHHhhcCCCC-CCccHHHHHHHHHHHhCCC-chHHHHHHH------HhccCC---HHHHHHHHHHHH
Q 039644          123 LEYHHALELFSQHAFKRNH-PDVGYEKLSSNVTKYAQGI-PLALKVLSC------FLHKRE---KEVWESAIDKLQ  187 (192)
Q Consensus       123 l~~~ea~~lf~~~~~~~~~-~~~~~~~~~~~i~~~~~g~-Plai~~~~~------~l~~~~---~~~w~~~l~~l~  187 (192)
                      .+.++..+++......... ....    ...+.+.+.|. |-.+..+..      ..+...   .+...++++++.
T Consensus       188 p~~~~r~~il~~~~~~~~~~~~~~----~~~l~~~~~g~~~~~i~~l~~~a~~~a~~~~~~~I~~~d~~~al~~~~  259 (285)
T 3h4m_A          188 PDEKGRLEILKIHTRKMNLAEDVN----LEEIAKMTEGCVGAELKAICTEAGMNAIRELRDYVTMDDFRKAVEKIM  259 (285)
T ss_dssp             CCHHHHHHHHHHHHTTSCBCTTCC----HHHHHHHCTTCCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhcCCCCCcCC----HHHHHHHcCCCCHHHHHHHHHHHHHHHHHhccCcCCHHHHHHHHHHHH
Confidence            9999999999887643222 1222    34566667764 434443322      222222   666666666554

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=97.46  E-value=0.0014  Score=50.37  Aligned_cols=131  Identities=10%  Similarity=0.096  Sum_probs=72.4

Q ss_pred             CchhHHHHHHHHHhhCCC-----c--ceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-cC---chHHHHhhc---C
Q 039644            1 IGKTAIARAIFDKISGDF-----E--CSCFLENVREESQRPGGLACLRQKLLSNILKDKNV-MP---YIDLNFRRL---S   66 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F-----~--~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~---~~~~l~~~l---~   66 (192)
                      +|||++++.+++++....     +  ..+.+.+...     .+...++..|.+++.+.... ..   .+..+...+   .
T Consensus        56 TGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~-----~t~~~~~~~I~~~L~g~~~~~~~~~~~L~~~f~~~~~~~  130 (318)
T 3te6_A           56 STKFQLVNDVMDELITSSARKELPIFDYIHIDALEL-----AGMDALYEKIWFAISKENLCGDISLEALNFYITNVPKAK  130 (318)
T ss_dssp             HHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCC-----C--HHHHHHHHHHHSCCC--CCCCHHHHHHHHHHSCGGG
T ss_pred             CCHHHHHHHHHHHHHHHhhhccCCceEEEEEecccc-----CCHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHhhhcc
Confidence            499999999999764321     1  2344442222     46778888999998654322 11   233333333   3


Q ss_pred             CceEEEEEeCCCCchh---HHHhhccCCCCCCCceEEEEecchh-----H----HhhcCCCceEecCCCCHHHHHHHHHH
Q 039644           67 RMKVLIVFDDVTCFSQ---LESLMGSLDWLTPVSRIILTTRNKQ-----V----LRNWGVSKIYEMEALEYHHALELFSQ  134 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~~---~~~l~~~~~~~~~~~~iivTtR~~~-----~----~~~~~~~~~~~l~~l~~~ea~~lf~~  134 (192)
                      +++++++||.++...+   +..+............+|.++....     +    ...++ ...+.+++.+.+|..+++..
T Consensus       131 ~~~~ii~lDE~d~l~~q~~L~~l~~~~~~~~s~~~vI~i~n~~d~~~~~L~~~v~SR~~-~~~i~F~pYt~~el~~Il~~  209 (318)
T 3te6_A          131 KRKTLILIQNPENLLSEKILQYFEKWISSKNSKLSIICVGGHNVTIREQINIMPSLKAH-FTEIKLNKVDKNELQQMIIT  209 (318)
T ss_dssp             SCEEEEEEECCSSSCCTHHHHHHHHHHHCSSCCEEEEEECCSSCCCHHHHHTCHHHHTT-EEEEECCCCCHHHHHHHHHH
T ss_pred             CCceEEEEecHHHhhcchHHHHHHhcccccCCcEEEEEEecCcccchhhcchhhhccCC-ceEEEeCCCCHHHHHHHHHH
Confidence            5689999999986532   2222211001111222333343321     1    11221 25799999999999999887


Q ss_pred             hhc
Q 039644          135 HAF  137 (192)
Q Consensus       135 ~~~  137 (192)
                      +..
T Consensus       210 Rl~  212 (318)
T 3te6_A          210 RLK  212 (318)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            653

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=97.42  E-value=0.0014  Score=52.81  Aligned_cols=141  Identities=16%  Similarity=0.212  Sum_probs=75.1

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +||||||+.+++.....|..   +. ...     ....++. .++....            .....+++.+|+||+++..
T Consensus        61 tGKTtlAr~ia~~~~~~f~~---l~-a~~-----~~~~~ir-~~~~~a~------------~~~~~~~~~iLfIDEI~~l  118 (447)
T 3pvs_A           61 TGKTTLAEVIARYANADVER---IS-AVT-----SGVKEIR-EAIERAR------------QNRNAGRRTILFVDEVHRF  118 (447)
T ss_dssp             SSHHHHHHHHHHHTTCEEEE---EE-TTT-----CCHHHHH-HHHHHHH------------HHHHTTCCEEEEEETTTCC
T ss_pred             CcHHHHHHHHHHHhCCCeEE---EE-ecc-----CCHHHHH-HHHHHHH------------HhhhcCCCcEEEEeChhhh
Confidence            69999999999987554422   11 111     2333322 2221111            1112456789999999865


Q ss_pred             h--hHHHhhccCCCCCCCceEEE-EecchhH---HhhcCCCceEecCCCCHHHHHHHHHHhhcCCC-----CCCccHHHH
Q 039644           81 S--QLESLMGSLDWLTPVSRIIL-TTRNKQV---LRNWGVSKIYEMEALEYHHALELFSQHAFKRN-----HPDVGYEKL  149 (192)
Q Consensus        81 ~--~~~~l~~~~~~~~~~~~iiv-TtR~~~~---~~~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~-----~~~~~~~~~  149 (192)
                      .  ..+.|...+.. + ...+|. ||.+...   .........+.+.+++.++...++........     ....-..+.
T Consensus       119 ~~~~q~~LL~~le~-~-~v~lI~att~n~~~~l~~aL~sR~~v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~a  196 (447)
T 3pvs_A          119 NKSQQDAFLPHIED-G-TITFIGATTENPSFELNSALLSRARVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDET  196 (447)
T ss_dssp             ------CCHHHHHT-T-SCEEEEEESSCGGGSSCHHHHTTEEEEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEECCHHH
T ss_pred             CHHHHHHHHHHHhc-C-ceEEEecCCCCcccccCHHHhCceeEEeeCCcCHHHHHHHHHHHHHHHhhhhccccCcCCHHH
Confidence            3  23344333332 1 223333 4444321   11113456889999999999999887654311     111223455


Q ss_pred             HHHHHHHhCCCchHHH
Q 039644          150 SSNVTKYAQGIPLALK  165 (192)
Q Consensus       150 ~~~i~~~~~g~Plai~  165 (192)
                      ...+++.++|.+..+.
T Consensus       197 l~~L~~~~~Gd~R~ll  212 (447)
T 3pvs_A          197 RRAIAELVNGDARRAL  212 (447)
T ss_dssp             HHHHHHHHCSCHHHHH
T ss_pred             HHHHHHHCCCCHHHHH
Confidence            6667777777766543

>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=97.41  E-value=0.0018  Score=53.10  Aligned_cols=154  Identities=15%  Similarity=0.147  Sum_probs=76.7

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHh--hcCCceEEEEEeCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFR--RLSRMKVLIVFDDVT   78 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~--~l~~~~~LlVlDdv~   78 (192)
                      +|||++|+.+++.+.  +. .+.+. .+.     .....+....+..................  ....++.+|+||+++
T Consensus        88 tGKTtla~~la~~l~--~~-~i~in-~s~-----~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~vliIDEid  158 (516)
T 1sxj_A           88 IGKTTAAHLVAQELG--YD-ILEQN-ASD-----VRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVD  158 (516)
T ss_dssp             SSHHHHHHHHHHHTT--CE-EEEEC-TTS-----CCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGG
T ss_pred             CCHHHHHHHHHHHcC--CC-EEEEe-CCC-----cchHHHHHHHHHHHhccccHHHHHhhhhhhhhccCCCeEEEEECCC
Confidence            699999999999873  22 22232 222     12222333332222211110111111100  123568899999997


Q ss_pred             Cch-----hHHHhhccCCCCCCCceEEEEecchh---HHhhcCCCceEecCCCCHHHHHHHHHHhhcCCCCCCccHHHHH
Q 039644           79 CFS-----QLESLMGSLDWLTPVSRIILTTRNKQ---VLRNWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLS  150 (192)
Q Consensus        79 ~~~-----~~~~l~~~~~~~~~~~~iivTtR~~~---~~~~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~  150 (192)
                      ...     .+..+...+..  .+..||+++....   ..........+.+++++.++..+++...+......  -..+..
T Consensus       159 ~l~~~~~~~l~~L~~~l~~--~~~~iIli~~~~~~~~l~~l~~r~~~i~f~~~~~~~~~~~L~~i~~~~~~~--i~~~~l  234 (516)
T 1sxj_A          159 GMSGGDRGGVGQLAQFCRK--TSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFK--LDPNVI  234 (516)
T ss_dssp             GCCTTSTTHHHHHHHHHHH--CSSCEEEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCC--CCTTHH
T ss_pred             ccchhhHHHHHHHHHHHHh--cCCCEEEEEcCCCCccchhhHhceEEEEeCCCCHHHHHHHHHHHHHHcCCC--CCHHHH
Confidence            542     12333322221  2334666654432   11112345679999999999998887765321110  112335


Q ss_pred             HHHHHHhCCCch-HHHHH
Q 039644          151 SNVTKYAQGIPL-ALKVL  167 (192)
Q Consensus       151 ~~i~~~~~g~Pl-ai~~~  167 (192)
                      ..|++.++|.+. ++..+
T Consensus       235 ~~la~~s~GdiR~~i~~L  252 (516)
T 1sxj_A          235 DRLIQTTRGDIRQVINLL  252 (516)
T ss_dssp             HHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHcCCcHHHHHHHH
Confidence            578888888544 44444

>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=97.39  E-value=0.015  Score=42.75  Aligned_cols=100  Identities=14%  Similarity=0.210  Sum_probs=53.5

Q ss_pred             CceEEEEEeCCCCch-----------------hHHHhhccCCC--CCCCceEEEEecchhHHhh--c---CCCceEecCC
Q 039644           67 RMKVLIVFDDVTCFS-----------------QLESLMGSLDW--LTPVSRIILTTRNKQVLRN--W---GVSKIYEMEA  122 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~-----------------~~~~l~~~~~~--~~~~~~iivTtR~~~~~~~--~---~~~~~~~l~~  122 (192)
                      ..+.+|+||+++...                 .+..+...+..  ...+..+|.||........  .   .....+.++.
T Consensus        97 ~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~~vi~~tn~~~~ld~~l~~~~R~~~~i~i~~  176 (262)
T 2qz4_A           97 RAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTDHVIVLASTNRADILDGALMRPGRLDRHVFIDL  176 (262)
T ss_dssp             TCSEEEEEECC-------------------CHHHHHHHHHHHTCCTTCCEEEEEEESCGGGGGSGGGSTTSCCEEEECCS
T ss_pred             cCCeEEEEeCcchhhccccccccCccchhHHHHHHHHHHHhhCcCCCCCEEEEecCCChhhcCHHHhcCCcCCeEEEeCC
Confidence            457899999998541                 12233222221  1234456666655432111  1   1235778899


Q ss_pred             CCHHHHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCCch-HHHHH
Q 039644          123 LEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPL-ALKVL  167 (192)
Q Consensus       123 l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~Pl-ai~~~  167 (192)
                      .+.++-.+++......... ..........+.+.+.|++- .|..+
T Consensus       177 p~~~~r~~il~~~~~~~~~-~~~~~~~~~~l~~~~~g~~~~~l~~l  221 (262)
T 2qz4_A          177 PTLQERREIFEQHLKSLKL-TQSSTFYSQRLAELTPGFSGADIANI  221 (262)
T ss_dssp             CCHHHHHHHHHHHHHHTTC-CBTHHHHHHHHHHTCTTCCHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHhCCC-CcchhhHHHHHHHHCCCCCHHHHHHH
Confidence            9999999988876532221 12222234678888888765 44433

>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=97.38  E-value=0.0016  Score=49.96  Aligned_cols=101  Identities=10%  Similarity=0.033  Sum_probs=56.2

Q ss_pred             CCceEEEEEeCCCCchh-------------HHHhhcc---CCCCCCCceEEEEecchhHHhh---cCCCceEecCCCCHH
Q 039644           66 SRMKVLIVFDDVTCFSQ-------------LESLMGS---LDWLTPVSRIILTTRNKQVLRN---WGVSKIYEMEALEYH  126 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~~~-------------~~~l~~~---~~~~~~~~~iivTtR~~~~~~~---~~~~~~~~l~~l~~~  126 (192)
                      ...+.+|+||+++....             ...+...   +.....+..||.||........   ......+.++..+.+
T Consensus       108 ~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~atn~~~~ld~al~~Rf~~~i~~~~p~~~  187 (322)
T 3eie_A          108 ENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLA  187 (322)
T ss_dssp             HTSSEEEEEECGGGGSCC------CCTHHHHHHHHHHHGGGGTSCCCEEEEEEESCGGGSCHHHHHHCCEEEECCCCCHH
T ss_pred             hcCCeEEEechhhhhhccCCCCcchHHHHHHHHHHHHhccccccCCceEEEEecCChhhCCHHHHcccCeEEEeCCCCHH
Confidence            34678999999974311             2222222   2222344555557765332111   023456788888999


Q ss_pred             HHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCC-chHHHHHH
Q 039644          127 HALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGI-PLALKVLS  168 (192)
Q Consensus       127 ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~-Plai~~~~  168 (192)
                      +-.+++.........  .........+++.+.|+ +-.|..+.
T Consensus       188 ~r~~il~~~~~~~~~--~~~~~~l~~la~~t~g~sg~di~~l~  228 (322)
T 3eie_A          188 ARTTMFEINVGDTPC--VLTKEDYRTLGAMTEGYSGSDIAVVV  228 (322)
T ss_dssp             HHHHHHHHHHTTCCC--CCCHHHHHHHHHTTTTCCHHHHHHHH
T ss_pred             HHHHHHHHHhccCCC--CCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            999999887643221  11234456788888874 43444443

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.38  E-value=0.0021  Score=49.72  Aligned_cols=99  Identities=6%  Similarity=0.058  Sum_probs=60.5

Q ss_pred             CceEEEEEeCCCCchh--HHHhhccCCCCCCCceEEEEecchhHH-hh-cCCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFSQ--LESLMGSLDWLTPVSRIILTTRNKQVL-RN-WGVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~~--~~~l~~~~~~~~~~~~iivTtR~~~~~-~~-~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      .++-++|||+++....  .+.+...+.....++.+|++|...... .. .+....+.+++++.++..+.+...+..... 
T Consensus       133 ~~~~vlilDE~~~L~~~~~~~L~~~le~~~~~~~~Il~t~~~~~l~~~l~sR~~~~~~~~~~~~~~~~~l~~~~~~~~~-  211 (354)
T 1sxj_E          133 HRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERI-  211 (354)
T ss_dssp             -CCEEEEEECTTSSCHHHHHHHHHHHHHSTTTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTC-
T ss_pred             CCCeEEEEeCccccCHHHHHHHHHHHHhhcCCCEEEEEeCCHHHHHHHHHhhceEEecCCcCHHHHHHHHHHHHHHcCC-
Confidence            3677999999987532  334443333333467788888664311 11 134478999999999999988876532111 


Q ss_pred             CccH-HHHHHHHHHHhCCCchHHHHH
Q 039644          143 DVGY-EKLSSNVTKYAQGIPLALKVL  167 (192)
Q Consensus       143 ~~~~-~~~~~~i~~~~~g~Plai~~~  167 (192)
                       .-. ++....|++.++|.+..+..+
T Consensus       212 -~~~~~~~l~~i~~~~~G~~r~a~~~  236 (354)
T 1sxj_E          212 -QLETKDILKRIAQASNGNLRVSLLM  236 (354)
T ss_dssp             -EECCSHHHHHHHHHHTTCHHHHHHH
T ss_pred             -CCCcHHHHHHHHHHcCCCHHHHHHH
Confidence             111 345567788888887655443

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=97.37  E-value=0.019  Score=44.07  Aligned_cols=100  Identities=12%  Similarity=0.073  Sum_probs=55.4

Q ss_pred             CceEEEEEeCCCCch-------------hHHHhhccCC---CCCCCceEEEEecchhHHhh---cCCCceEecCCCCHHH
Q 039644           67 RMKVLIVFDDVTCFS-------------QLESLMGSLD---WLTPVSRIILTTRNKQVLRN---WGVSKIYEMEALEYHH  127 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~-------------~~~~l~~~~~---~~~~~~~iivTtR~~~~~~~---~~~~~~~~l~~l~~~e  127 (192)
                      ..+.+|+||+++...             ....+...+.   ....+..||.||........   ......+.++..+.++
T Consensus       104 ~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~ld~~~~~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~  183 (322)
T 1xwi_A          104 NKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEPHA  183 (322)
T ss_dssp             TSSEEEEEETTTGGGCCSSSCCTTHHHHHHHHHHHHHHCSSSCCTTEEEEEEESCTTTSCHHHHHTCCEEEECCCCCHHH
T ss_pred             cCCcEEEeecHHHhccccccccchHHHHHHHHHHHHHhcccccCCCEEEEEecCCcccCCHHHHhhcCeEEEeCCcCHHH
Confidence            567899999997541             0122222221   11234445556654321111   1334678888889998


Q ss_pred             HHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCCch-HHHHHH
Q 039644          128 ALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPL-ALKVLS  168 (192)
Q Consensus       128 a~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~Pl-ai~~~~  168 (192)
                      -.+++.........  .........+++.+.|+.- .|..+.
T Consensus       184 r~~il~~~l~~~~~--~l~~~~l~~la~~t~G~sgadl~~l~  223 (322)
T 1xwi_A          184 RAAMFKLHLGTTQN--SLTEADFRELGRKTDGYSGADISIIV  223 (322)
T ss_dssp             HHHHHHHHHTTCCB--CCCHHHHHHHHHTCTTCCHHHHHHHH
T ss_pred             HHHHHHHHHhcCCC--CCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            88888876632221  1123456678888888743 354444

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=97.33  E-value=0.0047  Score=47.18  Aligned_cols=142  Identities=13%  Similarity=0.144  Sum_probs=74.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||++|+.+++.+..   ..+.+. .+.     ..... ....+.......+           +.+.+.++++|+++..
T Consensus        59 ~GKT~la~~la~~l~~---~~~~i~-~~~-----~~~~~-i~~~~~~~~~~~~-----------~~~~~~vliiDEi~~l  117 (324)
T 3u61_B           59 TGKTTVAKALCHDVNA---DMMFVN-GSD-----CKIDF-VRGPLTNFASAAS-----------FDGRQKVIVIDEFDRS  117 (324)
T ss_dssp             SSHHHHHHHHHHHTTE---EEEEEE-TTT-----CCHHH-HHTHHHHHHHBCC-----------CSSCEEEEEEESCCCG
T ss_pred             CCHHHHHHHHHHHhCC---CEEEEc-ccc-----cCHHH-HHHHHHHHHhhcc-----------cCCCCeEEEEECCccc
Confidence            6999999999998742   223333 222     23222 2222222211111           1246789999999976


Q ss_pred             h---hHHHhhccCCCCCCCceEEEEecchhHHhh--cCCCceEecCCCCHHHHHHHH-------HHhhcCCCCCCccHHH
Q 039644           81 S---QLESLMGSLDWLTPVSRIILTTRNKQVLRN--WGVSKIYEMEALEYHHALELF-------SQHAFKRNHPDVGYEK  148 (192)
Q Consensus        81 ~---~~~~l~~~~~~~~~~~~iivTtR~~~~~~~--~~~~~~~~l~~l~~~ea~~lf-------~~~~~~~~~~~~~~~~  148 (192)
                      .   ..+.+...+.....++++|+||........  ......+.+++++.++-.+++       ...+..... .-...+
T Consensus       118 ~~~~~~~~L~~~le~~~~~~~iI~~~n~~~~l~~~l~sR~~~i~~~~~~~~e~~~il~~~~~~l~~~~~~~~~-~~~~~~  196 (324)
T 3u61_B          118 GLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQSRCRVITFGQPTDEDKIEMMKQMIRRLTEICKHEGI-AIADMK  196 (324)
T ss_dssp             GGHHHHHHHHHHHHHHGGGCEEEEEESSGGGSCTTHHHHSEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHTC-CBSCHH
T ss_pred             CcHHHHHHHHHHHHhCCCCcEEEEEeCCccccCHHHHhhCcEEEeCCCCHHHHHHHHHHHHHHHHHHHHHcCC-CCCcHH
Confidence            4   344444333322345678888876441110  012357999999988743332       222211111 110125


Q ss_pred             HHHHHHHHhCCCchHH
Q 039644          149 LSSNVTKYAQGIPLAL  164 (192)
Q Consensus       149 ~~~~i~~~~~g~Plai  164 (192)
                      ....+++.++|.+..+
T Consensus       197 ~~~~l~~~~~gd~R~a  212 (324)
T 3u61_B          197 VVAALVKKNFPDFRKT  212 (324)
T ss_dssp             HHHHHHHHTCSCTTHH
T ss_pred             HHHHHHHhCCCCHHHH
Confidence            5667888888876643

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=97.29  E-value=0.0034  Score=47.56  Aligned_cols=69  Identities=10%  Similarity=0.073  Sum_probs=43.3

Q ss_pred             eEEEEEeCCCCc-----------hhHHHhhccCCCCCCCceEEEEecchhHHhh---c-----CCCceEecCCCCHHHHH
Q 039644           69 KVLIVFDDVTCF-----------SQLESLMGSLDWLTPVSRIILTTRNKQVLRN---W-----GVSKIYEMEALEYHHAL  129 (192)
Q Consensus        69 ~~LlVlDdv~~~-----------~~~~~l~~~~~~~~~~~~iivTtR~~~~~~~---~-----~~~~~~~l~~l~~~ea~  129 (192)
                      +.+|+||+++..           .....+...+.....+..+|.||........   .     .....+.+++++.++..
T Consensus       131 ~~vl~iDEid~l~~~~~~~~~~~~~~~~Ll~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~R~~~~i~~~~~~~~~~~  210 (309)
T 3syl_A          131 GGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENNRDDLVVILAGYADRMENFFQSNPGFRSRIAHHIEFPDYSDEELF  210 (309)
T ss_dssp             TSEEEEETGGGSCCCC---CCTHHHHHHHHHHHHHCTTTCEEEEEECHHHHHHHHHHSTTHHHHEEEEEEECCCCHHHHH
T ss_pred             CCEEEEEChhhhccCCCcccccHHHHHHHHHHHhcCCCCEEEEEeCChHHHHHHHhhCHHHHHhCCeEEEcCCcCHHHHH
Confidence            459999999833           2344444444434456677777754321110   0     12367899999999999


Q ss_pred             HHHHHhhc
Q 039644          130 ELFSQHAF  137 (192)
Q Consensus       130 ~lf~~~~~  137 (192)
                      .++.....
T Consensus       211 ~il~~~l~  218 (309)
T 3syl_A          211 EIAGHMLD  218 (309)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99877653

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=97.28  E-value=0.0064  Score=48.84  Aligned_cols=101  Identities=12%  Similarity=0.072  Sum_probs=57.3

Q ss_pred             CCceEEEEEeCCCCch-------------hHHHhhccCCC---CCCCceEEEEecchhHHhh---cCCCceEecCCCCHH
Q 039644           66 SRMKVLIVFDDVTCFS-------------QLESLMGSLDW---LTPVSRIILTTRNKQVLRN---WGVSKIYEMEALEYH  126 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~~-------------~~~~l~~~~~~---~~~~~~iivTtR~~~~~~~---~~~~~~~~l~~l~~~  126 (192)
                      ...+.+|+||+++...             ....+...+..   ...+..||.||........   ......+.++..+.+
T Consensus       225 ~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~  304 (444)
T 2zan_A          225 ENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEAH  304 (444)
T ss_dssp             HSCSEEEEESCTTTTCCCSSCCCCGGGHHHHHHHHTTTTCSSCCCSSCEEEEEESCGGGSCHHHHTTCCEEEECCCCCHH
T ss_pred             HcCCeEEEEechHhhccCCCCccccHHHHHHHHHHHHHhCcccCCCCEEEEecCCCccccCHHHHhhcceEEEeCCcCHH
Confidence            3567899999998541             12344443332   1344556667755432111   123457788888888


Q ss_pred             HHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCCch-HHHHHH
Q 039644          127 HALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPL-ALKVLS  168 (192)
Q Consensus       127 ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~Pl-ai~~~~  168 (192)
                      +...+|.........  .........|++.+.|+.- .|..+.
T Consensus       305 ~r~~il~~~l~~~~~--~l~~~~l~~la~~t~G~sgadl~~l~  345 (444)
T 2zan_A          305 ARAAMFRLHLGSTQN--SLTEADFQELGRKTDGYSGADISIIV  345 (444)
T ss_dssp             HHHHHHHHHHTTSCE--ECCHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCC--CCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            888888876632221  1123456678888888543 444433

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=97.17  E-value=0.005  Score=47.94  Aligned_cols=100  Identities=10%  Similarity=0.028  Sum_probs=55.1

Q ss_pred             CceEEEEEeCCCCchh-------------HHHhhcc---CCCCCCCceEEEEecchhHH---hhcCCCceEecCCCCHHH
Q 039644           67 RMKVLIVFDDVTCFSQ-------------LESLMGS---LDWLTPVSRIILTTRNKQVL---RNWGVSKIYEMEALEYHH  127 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~~-------------~~~l~~~---~~~~~~~~~iivTtR~~~~~---~~~~~~~~~~l~~l~~~e  127 (192)
                      ..+.+|+||+++....             ...+...   +.....+..||.||......   ........+.++..+.++
T Consensus       142 ~~~~vl~iDEid~l~~~r~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~  221 (355)
T 2qp9_X          142 NKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAA  221 (355)
T ss_dssp             TSSEEEEEECGGGGTC------CTHHHHHHHHHHHHHHHCC---CCEEEEEEESCGGGSCHHHHHTCCEEEECCCCCHHH
T ss_pred             cCCeEEEEechHhhcccCCCCcchHHHHHHHHHHHHhhcccccCCCeEEEeecCCcccCCHHHHcccCEEEEeCCcCHHH
Confidence            4678999999985320             2222222   21223345555566544211   111345678888889999


Q ss_pred             HHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCC-chHHHHHH
Q 039644          128 ALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGI-PLALKVLS  168 (192)
Q Consensus       128 a~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~-Plai~~~~  168 (192)
                      -.+++.........  .........|++.+.|. +-.|..+.
T Consensus       222 r~~il~~~l~~~~~--~~~~~~l~~la~~t~G~sg~dl~~l~  261 (355)
T 2qp9_X          222 RTTMFEINVGDTPS--VLTKEDYRTLGAMTEGYSGSDIAVVV  261 (355)
T ss_dssp             HHHHHHHHHTTSCB--CCCHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             HHHHHHHHHhhCCC--CCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            88988877633221  11234466788888885 33344443

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=97.15  E-value=0.016  Score=45.14  Aligned_cols=100  Identities=11%  Similarity=0.064  Sum_probs=54.0

Q ss_pred             CceEEEEEeCCCCc-------------hhHHHhhccCCC----CCCCceEEEEecchhHHh---hcCCCceEecCCCCHH
Q 039644           67 RMKVLIVFDDVTCF-------------SQLESLMGSLDW----LTPVSRIILTTRNKQVLR---NWGVSKIYEMEALEYH  126 (192)
Q Consensus        67 ~~~~LlVlDdv~~~-------------~~~~~l~~~~~~----~~~~~~iivTtR~~~~~~---~~~~~~~~~l~~l~~~  126 (192)
                      ..+.+|+||+++..             .....+...+..    ...+..||.||.......   .......+.+...+.+
T Consensus       175 ~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~Rf~~~i~i~~p~~~  254 (357)
T 3d8b_A          175 QQPAVIFIDEIDSLLSQRGDGEHESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAARRRLVKRLYIPLPEAS  254 (357)
T ss_dssp             TCSEEEEEETHHHHTBC------CHHHHHHHHHHHHHHC----CCCCEEEEEEESCGGGBCHHHHTTCCEEEECCCCCHH
T ss_pred             cCCeEEEEeCchhhhccCCCCcchHHHHHHHHHHHHHhcccccCCCCEEEEEecCChhhCCHHHHhhCceEEEeCCcCHH
Confidence            45789999999532             012222222211    123444555665432111   1123456788888988


Q ss_pred             HHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCC-chHHHHHH
Q 039644          127 HALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGI-PLALKVLS  168 (192)
Q Consensus       127 ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~-Plai~~~~  168 (192)
                      +..+++...+.....  .........+++.+.|+ +-.+..+.
T Consensus       255 ~r~~il~~~~~~~~~--~l~~~~l~~la~~t~G~s~~dl~~l~  295 (357)
T 3d8b_A          255 ARKQIVINLMSKEQC--CLSEEEIEQIVQQSDAFSGADMTQLC  295 (357)
T ss_dssp             HHHHHHHHHHHTSCB--CCCHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHhhcCC--CccHHHHHHHHHHcCCCCHHHHHHHH
Confidence            888888776532221  11234566788888884 44555554

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=97.15  E-value=0.023  Score=44.67  Aligned_cols=52  Identities=15%  Similarity=0.074  Sum_probs=34.2

Q ss_pred             CceEecCCCCHHHHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCCch-HHHHHH
Q 039644          115 SKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPL-ALKVLS  168 (192)
Q Consensus       115 ~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~Pl-ai~~~~  168 (192)
                      ...+.+...+.++..+++...+.....  .........+++.+.|..- ++..+.
T Consensus       274 ~~~i~i~~p~~~~r~~il~~~~~~~~~--~l~~~~~~~la~~~~g~~~~~l~~L~  326 (389)
T 3vfd_A          274 IKRVYVSLPNEETRLLLLKNLLCKQGS--PLTQKELAQLARMTDGYSGSDLTALA  326 (389)
T ss_dssp             CEEEECCCCCHHHHHHHHHHHHTTSCC--CSCHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             ceEEEcCCcCHHHHHHHHHHHHHhcCC--CCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            456888999999999998876633221  1223456678888888655 555544

>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=97.10  E-value=0.011  Score=45.66  Aligned_cols=95  Identities=9%  Similarity=0.087  Sum_probs=54.8

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchhHH-hh-cCCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQVL-RN-WGVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~~~-~~-~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +.+-++|+|+++...  ..+.+...+......+++|++|...... .. .+....+.+.+++.++..+.+...+-.... 
T Consensus       109 ~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~n~~~~i~~~i~sR~~~~~~~~l~~~~~~~~l~~~~~~~~~-  187 (340)
T 1sxj_C          109 KGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKL-  187 (340)
T ss_dssp             CSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHTTTC-
T ss_pred             CCceEEEEeCCCCCCHHHHHHHHHHHhcCCCCeEEEEEecCccccchhHHhhceeEeccCCCHHHHHHHHHHHHHHcCC-
Confidence            346789999997542  3344443333334556777777553311 11 133457889999999988877765522111 


Q ss_pred             CccHHHHHHHHHHHhCCCchH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Pla  163 (192)
                       .-.......+++.++|.+--
T Consensus       188 -~i~~~~~~~i~~~s~G~~r~  207 (340)
T 1sxj_C          188 -KLSPNAEKALIELSNGDMRR  207 (340)
T ss_dssp             -CBCHHHHHHHHHHHTTCHHH
T ss_pred             -CCCHHHHHHHHHHcCCCHHH
Confidence             11234455677777777653

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=96.99  E-value=0.00046  Score=48.12  Aligned_cols=65  Identities=8%  Similarity=-0.005  Sum_probs=35.8

Q ss_pred             CCceEEEEEeCCCCch---------h-HHHhhccCCCCCCCceEEEEecchhHHhh-------cCCCceEecCCCCHHHH
Q 039644           66 SRMKVLIVFDDVTCFS---------Q-LESLMGSLDWLTPVSRIILTTRNKQVLRN-------WGVSKIYEMEALEYHHA  128 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~~---------~-~~~l~~~~~~~~~~~~iivTtR~~~~~~~-------~~~~~~~~l~~l~~~ea  128 (192)
                      .+++.+|+||+++...         . ...+...+ . ..+..+|.+|........       ...-..+.+.+++.++.
T Consensus       113 ~~~~~vl~iDe~~~l~~~~~~~~~~~~~~~l~~~~-~-~~~~~~i~~~~~~~~~~~~~~~~~l~~r~~~i~~~~p~~~~~  190 (195)
T 1jbk_A          113 QEGNVILFIDELHTMVGAGKADGAMDAGNMLKPAL-A-RGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPSVEDT  190 (195)
T ss_dssp             STTTEEEEEETGGGGTT------CCCCHHHHHHHH-H-TTSCCEEEEECHHHHHHHTTTCHHHHTTEEEEECCCCCHHHH
T ss_pred             cCCCeEEEEeCHHHHhccCcccchHHHHHHHHHhh-c-cCCeEEEEeCCHHHHHHHHhcCHHHHHHhceeecCCCCHHHH
Confidence            3567899999997542         1 22222211 1 234457777765542211       12223578888888877


Q ss_pred             HHHH
Q 039644          129 LELF  132 (192)
Q Consensus       129 ~~lf  132 (192)
                      .+++
T Consensus       191 ~~il  194 (195)
T 1jbk_A          191 IAIL  194 (195)
T ss_dssp             HTTC
T ss_pred             HHHh
Confidence            6553

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=96.93  E-value=0.0096  Score=45.69  Aligned_cols=98  Identities=18%  Similarity=0.186  Sum_probs=56.4

Q ss_pred             ceEEEEEeCCCCch--hHHHhhccCCCC------------------CCCceEEEEecchhHHhh--c-CCCceEecCCCC
Q 039644           68 MKVLIVFDDVTCFS--QLESLMGSLDWL------------------TPVSRIILTTRNKQVLRN--W-GVSKIYEMEALE  124 (192)
Q Consensus        68 ~~~LlVlDdv~~~~--~~~~l~~~~~~~------------------~~~~~iivTtR~~~~~~~--~-~~~~~~~l~~l~  124 (192)
                      ...+|+||+++...  ....+...+...                  .+...+|.+|........  . .....+.+.+++
T Consensus       106 ~~~vl~lDEi~~l~~~~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~i~atn~~~~l~~~L~~R~~~~i~l~~~~  185 (338)
T 3pfi_A          106 EGDILFIDEIHRLSPAIEEVLYPAMEDYRLDIIIGSGPAAQTIKIDLPKFTLIGATTRAGMLSNPLRDRFGMQFRLEFYK  185 (338)
T ss_dssp             TTCEEEEETGGGCCHHHHHHHHHHHHTSCC---------CCCCCCCCCCCEEEEEESCGGGSCHHHHTTCSEEEECCCCC
T ss_pred             CCCEEEEechhhcCHHHHHHHHHHHHhccchhhcccCccccceecCCCCeEEEEeCCCccccCHHHHhhcCEEeeCCCcC
Confidence            45689999998542  222222211110                  112456666655332111  1 223679999999


Q ss_pred             HHHHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCCchHHHHH
Q 039644          125 YHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVL  167 (192)
Q Consensus       125 ~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plai~~~  167 (192)
                      .++...++...+....  .....+....+.+.+.|.|-.+..+
T Consensus       186 ~~e~~~il~~~~~~~~--~~~~~~~~~~l~~~~~G~~r~l~~~  226 (338)
T 3pfi_A          186 DSELALILQKAALKLN--KTCEEKAALEIAKRSRSTPRIALRL  226 (338)
T ss_dssp             HHHHHHHHHHHHHHTT--CEECHHHHHHHHHTTTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcC--CCCCHHHHHHHHHHHCcCHHHHHHH
Confidence            9999999887663222  1223455667888889998554433

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=96.86  E-value=0.0096  Score=46.18  Aligned_cols=95  Identities=9%  Similarity=0.025  Sum_probs=54.4

Q ss_pred             eEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecc------------hh-H-HhhcCCCceEecCCCCHHHHHHHH
Q 039644           69 KVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRN------------KQ-V-LRNWGVSKIYEMEALEYHHALELF  132 (192)
Q Consensus        69 ~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~------------~~-~-~~~~~~~~~~~l~~l~~~ea~~lf  132 (192)
                      +.+|+||+++...  ....+...+...... .++++|..            .. + .........+.+++++.++..+++
T Consensus       190 ~~vl~IDEi~~l~~~~~~~L~~~le~~~~~-~~ii~t~~~~~~i~~t~~~~~~~l~~~l~sR~~~i~~~~~~~~e~~~il  268 (368)
T 3uk6_A          190 PGVLFIDEVHMLDIESFSFLNRALESDMAP-VLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQIL  268 (368)
T ss_dssp             BCEEEEESGGGSBHHHHHHHHHHTTCTTCC-EEEEEESCSEEECBTSSCEEETTCCHHHHTTEEEEEECCCCHHHHHHHH
T ss_pred             CceEEEhhccccChHHHHHHHHHhhCcCCC-eeeeecccceeeeeccCCCCcccCCHHHHhhccEEEecCCCHHHHHHHH
Confidence            4699999998653  344444444332222 34444431            10 0 111123345899999999999999


Q ss_pred             HHhhcCCCCCCccHHHHHHHHHHHhC-CCchHHHH
Q 039644          133 SQHAFKRNHPDVGYEKLSSNVTKYAQ-GIPLALKV  166 (192)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~i~~~~~-g~Plai~~  166 (192)
                      ...+....  ..-..+....+++.+. |.|..+..
T Consensus       269 ~~~~~~~~--~~~~~~~l~~l~~~~~~G~~r~~~~  301 (368)
T 3uk6_A          269 RIRCEEED--VEMSEDAYTVLTRIGLETSLRYAIQ  301 (368)
T ss_dssp             HHHHHHTT--CCBCHHHHHHHHHHHHHSCHHHHHH
T ss_pred             HHHHHHcC--CCCCHHHHHHHHHHhcCCCHHHHHH
Confidence            87664322  1223455667788887 77765443

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=96.86  E-value=0.063  Score=40.24  Aligned_cols=98  Identities=15%  Similarity=0.099  Sum_probs=52.6

Q ss_pred             CceEEEEEeCCCCch-------------hHHHhh---ccCCCC--CCCceEEEEecchh-----HHhhcCCCceEecCCC
Q 039644           67 RMKVLIVFDDVTCFS-------------QLESLM---GSLDWL--TPVSRIILTTRNKQ-----VLRNWGVSKIYEMEAL  123 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~-------------~~~~l~---~~~~~~--~~~~~iivTtR~~~-----~~~~~~~~~~~~l~~l  123 (192)
                      ..+.+|+||+++...             ....+.   ..++..  +.+..||.||....     +..  .....+.++..
T Consensus       112 ~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~v~vi~~tn~~~~l~~~l~~--R~~~~i~~~~p  189 (297)
T 3b9p_A          112 MQPSIIFIDEVDSLLSERSSSEHEASRRLKTEFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALR--RFTKRVYVSLP  189 (297)
T ss_dssp             TCSEEEEEETGGGTSBCC-----CCSHHHHHHHHHHHHHCC------CEEEEEEESCGGGBCHHHHH--HCCEEEECCCC
T ss_pred             cCCcEEEeccHHHhccccccCcchHHHHHHHHHHHHHhcccccCCCCcEEEEeecCChhhCCHHHHh--hCCeEEEeCCc
Confidence            457899999996431             011121   112221  13345666676532     122  22356778878


Q ss_pred             CHHHHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCCch-HHHHHH
Q 039644          124 EYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPL-ALKVLS  168 (192)
Q Consensus       124 ~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~Pl-ai~~~~  168 (192)
                      +.++...++.........  .........+.+.+.|.+- ++..+.
T Consensus       190 ~~~~r~~il~~~~~~~~~--~~~~~~~~~la~~~~g~~~~~l~~l~  233 (297)
T 3b9p_A          190 DEQTRELLLNRLLQKQGS--PLDTEALRRLAKITDGYSGSDLTALA  233 (297)
T ss_dssp             CHHHHHHHHHHHHGGGSC--CSCHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhcCC--CCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            888888887765532111  1123456678888888876 454443

>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=96.66  E-value=0.0034  Score=43.74  Aligned_cols=88  Identities=19%  Similarity=0.224  Sum_probs=44.7

Q ss_pred             CchhHHHHHHHHHhh-CCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKIS-GDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~-~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~   79 (192)
                      +||||||+.++..+. ..-..++++.           ..++...+..........     .+...+. ++-+||||+++.
T Consensus        49 ~GKTtL~~~i~~~~~~~~g~~~~~~~-----------~~~~~~~~~~~~~~~~~~-----~~~~~~~-~~~llilDE~~~  111 (180)
T 3ec2_A           49 VGKTHLAVATLKAIYEKKGIRGYFFD-----------TKDLIFRLKHLMDEGKDT-----KFLKTVL-NSPVLVLDDLGS  111 (180)
T ss_dssp             SSHHHHHHHHHHHHHHHSCCCCCEEE-----------HHHHHHHHHHHHHHTCCS-----HHHHHHH-TCSEEEEETCSS
T ss_pred             CCHHHHHHHHHHHHHHHcCCeEEEEE-----------HHHHHHHHHHHhcCchHH-----HHHHHhc-CCCEEEEeCCCC
Confidence            699999999999764 2212233443           334444444333322211     1222222 456899999973


Q ss_pred             --chhHH--HhhccCCC-CCCCceEEEEecc
Q 039644           80 --FSQLE--SLMGSLDW-LTPVSRIILTTRN  105 (192)
Q Consensus        80 --~~~~~--~l~~~~~~-~~~~~~iivTtR~  105 (192)
                        .+.|.  .+...+.. ...+..+|+||..
T Consensus       112 ~~~~~~~~~~l~~ll~~~~~~~~~ii~tsn~  142 (180)
T 3ec2_A          112 ERLSDWQRELISYIITYRYNNLKSTIITTNY  142 (180)
T ss_dssp             SCCCHHHHHHHHHHHHHHHHTTCEEEEECCC
T ss_pred             CcCCHHHHHHHHHHHHHHHHcCCCEEEEcCC
Confidence              23322  22111111 1245678888864

>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=96.58  E-value=0.021  Score=43.23  Aligned_cols=140  Identities=14%  Similarity=0.186  Sum_probs=71.0

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||+||+.++......|   +.+           +..++..    ...+.... .....+.......+.+|+||+++..
T Consensus        60 tGKT~la~ala~~~~~~~---i~v-----------~~~~l~~----~~~g~~~~-~~~~~f~~a~~~~p~il~iDEid~l  120 (301)
T 3cf0_A           60 CGKTLLAKAIANECQANF---ISI-----------KGPELLT----MWFGESEA-NVREIFDKARQAAPCVLFFDELDSI  120 (301)
T ss_dssp             SSHHHHHHHHHHHTTCEE---EEE-----------CHHHHHH----HHHTTCTT-HHHHHHHHHHHTCSEEEEECSTTHH
T ss_pred             cCHHHHHHHHHHHhCCCE---EEE-----------EhHHHHh----hhcCchHH-HHHHHHHHHHhcCCeEEEEEChHHH
Confidence            699999999999875322   222           1222222    12221111 0112222222356899999999742


Q ss_pred             h----------------hHHHhhccCCC--CCCCceEEEEecchhHHhh--c---CCCceEecCCCCHHHHHHHHHHhhc
Q 039644           81 S----------------QLESLMGSLDW--LTPVSRIILTTRNKQVLRN--W---GVSKIYEMEALEYHHALELFSQHAF  137 (192)
Q Consensus        81 ~----------------~~~~l~~~~~~--~~~~~~iivTtR~~~~~~~--~---~~~~~~~l~~l~~~ea~~lf~~~~~  137 (192)
                      .                ....+...+..  ...+..||.||........  .   .....+.++..+.++-.+++.....
T Consensus       121 ~~~~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~v~vi~atn~~~~ld~al~r~gRf~~~i~i~~p~~~~r~~il~~~l~  200 (301)
T 3cf0_A          121 AKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLR  200 (301)
T ss_dssp             HHHHTTTTCCSSCSCCHHHHHHHHHHHSSCTTSSEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHT
T ss_pred             hhccCCCcCCcchHHHHHHHHHHHHhhcccCCCCEEEEEecCCccccChHHhcCCccceEEecCCcCHHHHHHHHHHHHc
Confidence            1                01223222211  1234566667765432211  1   2345788999999988888876653


Q ss_pred             CCCC-CCccHHHHHHHHHHHhCCCchH
Q 039644          138 KRNH-PDVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       138 ~~~~-~~~~~~~~~~~i~~~~~g~Pla  163 (192)
                      .... .+..+    ..+.+.+.|+|-+
T Consensus       201 ~~~~~~~~~~----~~la~~~~g~sg~  223 (301)
T 3cf0_A          201 KSPVAKDVDL----EFLAKMTNGFSGA  223 (301)
T ss_dssp             TSCBCSSCCH----HHHHHTCSSCCHH
T ss_pred             cCCCCccchH----HHHHHHcCCCCHH
Confidence            2221 12222    2445556666543

>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=96.53  E-value=0.016  Score=44.15  Aligned_cols=118  Identities=8%  Similarity=0.083  Sum_probs=70.7

Q ss_pred             CchhHHHHHHHHHh---hCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCC
Q 039644            1 IGKTAIARAIFDKI---SGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDV   77 (192)
Q Consensus         1 iGKTtLa~~~~~~~---~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv   77 (192)
                      +|||++|+.+++..   .........+. ...  .. ..+.++ +.+.+.....+.            .+++-++|+|++
T Consensus        29 ~GKtt~a~~la~~~~~~~~~~~d~~~l~-~~~--~~-~~id~i-r~li~~~~~~p~------------~~~~kvviIdea   91 (305)
T 2gno_A           29 SYPREVSLELPEYVEKFPPKASDVLEID-PEG--EN-IGIDDI-RTIKDFLNYSPE------------LYTRKYVIVHDC   91 (305)
T ss_dssp             SHHHHHHHHHHHHHHTSCCCTTTEEEEC-CSS--SC-BCHHHH-HHHHHHHTSCCS------------SSSSEEEEETTG
T ss_pred             CCHHHHHHHHHHhCchhhccCCCEEEEc-CCc--CC-CCHHHH-HHHHHHHhhccc------------cCCceEEEeccH
Confidence            59999999998853   22233445554 211  01 233333 334444432111            245678999999


Q ss_pred             CCch--hHHHhhccCCCCCCCceEEEEecchh-HHhhcCCCceEecCCCCHHHHHHHHHHhh
Q 039644           78 TCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRNWGVSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus        78 ~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~~~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      +...  ..+.+...+....+.+.+|++|.+.. +....... .+++++++.++..+.+....
T Consensus        92 d~lt~~a~naLLk~LEep~~~t~fIl~t~~~~kl~~tI~SR-~~~f~~l~~~~i~~~L~~~~  152 (305)
T 2gno_A           92 ERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSR-VFRVVVNVPKEFRDLVKEKI  152 (305)
T ss_dssp             GGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTT-SEEEECCCCHHHHHHHHHHH
T ss_pred             HHhCHHHHHHHHHHHhCCCCCeEEEEEECChHhChHHHHce-eEeCCCCCHHHHHHHHHHHh
Confidence            8653  45666666555556778888876543 22222222 89999999999998887764

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=96.27  E-value=0.016  Score=41.22  Aligned_cols=121  Identities=17%  Similarity=0.121  Sum_probs=61.3

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHH-------hcCCCC--------cCchHHHHhhc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNI-------LKDKNV--------MPYIDLNFRRL   65 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~-------~~~~~~--------~~~~~~l~~~l   65 (192)
                      .||||+|.-++.+...+=..+.++..+... .. ..-.+++..+.-.+       ....+.        .......++.+
T Consensus        39 kGKTTaA~GlalRA~g~G~rV~~vQF~Kg~-~~-~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~a~~~l~~a~~~l  116 (196)
T 1g5t_A           39 KGKTTAAFGTAARAVGHGKNVGVVQFIKGT-WP-NGERNLLEPHGVEFQVMATGFTWETQNREADTAACMAVWQHGKRML  116 (196)
T ss_dssp             SCHHHHHHHHHHHHHHTTCCEEEEESSCCS-SC-CHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHCCCeEEEEEeeCCC-CC-ccHHHHHHhCCcEEEEcccccccCCCCcHHHHHHHHHHHHHHHHHH
Confidence            499999999999855443344444323220 11 23333333331000       000000        00455566666


Q ss_pred             CCceE-EEEEeCCCCc-----hhHHHhhccCCCCCCCceEEEEecchhHHhhcCCCceEecCCC
Q 039644           66 SRMKV-LIVFDDVTCF-----SQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEMEAL  123 (192)
Q Consensus        66 ~~~~~-LlVlDdv~~~-----~~~~~l~~~~~~~~~~~~iivTtR~~~~~~~~~~~~~~~l~~l  123 (192)
                      .+.+| |||||.+...     -..+.+...+........||+|+|.....-..-...+-+|...
T Consensus       117 ~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~ap~~l~e~AD~VTem~~v  180 (196)
T 1g5t_A          117 ADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILDLADTVSELRPV  180 (196)
T ss_dssp             TCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHHHHCSEEEECCCS
T ss_pred             hcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCCcHHHHHhCcceeeecce
Confidence            66655 9999999432     1123333333333456789999998654333333445555544

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.22  E-value=0.12  Score=40.94  Aligned_cols=139  Identities=19%  Similarity=0.217  Sum_probs=73.8

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCC-ChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPG-GLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~   79 (192)
                      +|||.||+.++......|   +.++ .+....... .....++.+                +...-...+++|.||+++.
T Consensus       193 TGKTllAkAiA~e~~~~f---~~v~-~s~l~sk~vGese~~vr~l----------------F~~Ar~~aP~IIFiDEiDa  252 (405)
T 4b4t_J          193 TGKTLLARAVAHHTDCKF---IRVS-GAELVQKYIGEGSRMVREL----------------FVMAREHAPSIIFMDEIDS  252 (405)
T ss_dssp             SSHHHHHHHHHHHHTCEE---EEEE-GGGGSCSSTTHHHHHHHHH----------------HHHHHHTCSEEEEEESSSC
T ss_pred             CCHHHHHHHHHHhhCCCc---eEEE-hHHhhccccchHHHHHHHH----------------HHHHHHhCCceEeeecchh
Confidence            699999999999876654   2232 222111100 011111111                1222235689999999974


Q ss_pred             ch------------h----HHHhhccCCCC--CCCceEEEEecchhHHhh-----cCCCceEecCCCCHHHHHHHHHHhh
Q 039644           80 FS------------Q----LESLMGSLDWL--TPVSRIILTTRNKQVLRN-----WGVSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus        80 ~~------------~----~~~l~~~~~~~--~~~~~iivTtR~~~~~~~-----~~~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      ..            .    ...+...+...  ..+..||.||........     ......+.++..+.++-.++|+.+.
T Consensus       253 i~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~  332 (405)
T 4b4t_J          253 IGSTRVEGSGGGDSEVQRTMLELLNQLDGFETSKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHS  332 (405)
T ss_dssp             CTTSCSCSSSGGGGHHHHHHHHHHHHHHTTTCCCCEEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHH
T ss_pred             hccCCCCCCCCCcHHHHHHHHHHHHhhhccCCCCCeEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHh
Confidence            21            0    22333333222  234455667765442211     1235678888888888888888765


Q ss_pred             cCCCC-CCccHHHHHHHHHHHhCCCchH
Q 039644          137 FKRNH-PDVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       137 ~~~~~-~~~~~~~~~~~i~~~~~g~Pla  163 (192)
                      ..-.. .+..+    ..+++.+.|+--|
T Consensus       333 ~~~~l~~dvdl----~~lA~~t~G~SGA  356 (405)
T 4b4t_J          333 RKMNLTRGINL----RKVAEKMNGCSGA  356 (405)
T ss_dssp             TTSBCCSSCCH----HHHHHHCCSCCHH
T ss_pred             cCCCCCccCCH----HHHHHHCCCCCHH
Confidence            33221 12223    4577778877544

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=96.09  E-value=0.038  Score=41.68  Aligned_cols=25  Identities=20%  Similarity=0.325  Sum_probs=17.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +|||++|+.++......-...+.+.
T Consensus        58 tGKt~la~~la~~~~~~~~~~~~~~   82 (311)
T 4fcw_A           58 VGKTELAKTLAATLFDTEEAMIRID   82 (311)
T ss_dssp             SSHHHHHHHHHHHHHSCGGGEEEEE
T ss_pred             cCHHHHHHHHHHHHcCCCcceEEee
Confidence            6999999999997644323334444

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=95.97  E-value=0.011  Score=41.79  Aligned_cols=25  Identities=24%  Similarity=0.270  Sum_probs=19.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +|||+||+.++.........++++.
T Consensus        65 tGKT~la~~i~~~~~~~~~~~~~~~   89 (202)
T 2w58_A           65 VGKTYLLAAIANELAKRNVSSLIVY   89 (202)
T ss_dssp             SSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             CCHHHHHHHHHHHHHHcCCeEEEEE
Confidence            6999999999998765544556664

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.73  E-value=0.072  Score=42.64  Aligned_cols=139  Identities=21%  Similarity=0.263  Sum_probs=73.5

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCC-hHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGG-LACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~   79 (192)
                      +|||.||+.++......|-   .++ .+........ .....+.                .+...-...+++|.+|+++.
T Consensus       226 tGKTllAkAiA~e~~~~~~---~v~-~s~l~sk~~Gese~~ir~----------------~F~~A~~~~P~IifiDEiDa  285 (437)
T 4b4t_L          226 TGKTLLAKAVAATIGANFI---FSP-ASGIVDKYIGESARIIRE----------------MFAYAKEHEPCIIFMDEVDA  285 (437)
T ss_dssp             SSHHHHHHHHHHHHTCEEE---EEE-GGGTCCSSSSHHHHHHHH----------------HHHHHHHSCSEEEEEECCCS
T ss_pred             CcHHHHHHHHHHHhCCCEE---EEe-hhhhccccchHHHHHHHH----------------HHHHHHhcCCceeeeecccc
Confidence            6999999999998765432   222 2221111011 1111111                12222235689999999973


Q ss_pred             ch------------h----HHHhhccCCC--CCCCceEEEEecchhHHhhc--C---CCceEecCCCCHHHHHHHHHHhh
Q 039644           80 FS------------Q----LESLMGSLDW--LTPVSRIILTTRNKQVLRNW--G---VSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus        80 ~~------------~----~~~l~~~~~~--~~~~~~iivTtR~~~~~~~~--~---~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      ..            .    +..+...+..  ...+..||.||.........  .   ....+.++..+.++-.++|..+.
T Consensus       286 i~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~vivI~ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~  365 (437)
T 4b4t_L          286 IGGRRFSEGTSADREIQRTLMELLTQMDGFDNLGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHT  365 (437)
T ss_dssp             SSCCCSSSCCSSTTHHHHHHHHHHHHHHSSSCTTSSEEEEEESSTTSSCTTTTSTTSEEEEECCCCCCHHHHHHHHHHHH
T ss_pred             cccccccCCCCcchHHHHHHHHHHHHhhcccCCCCeEEEEecCCchhhCHHHhCCCccceeeecCCcCHHHHHHHHHHHh
Confidence            21            0    2233333322  22345677777665433221  1   24567888888888888887765


Q ss_pred             cCCC-CCCccHHHHHHHHHHHhCCCchH
Q 039644          137 FKRN-HPDVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       137 ~~~~-~~~~~~~~~~~~i~~~~~g~Pla  163 (192)
                      ..-. ..+..+    ..+++.+.|+--|
T Consensus       366 ~~~~~~~d~dl----~~lA~~t~G~sGA  389 (437)
T 4b4t_L          366 AKVKKTGEFDF----EAAVKMSDGFNGA  389 (437)
T ss_dssp             HTSCBCSCCCH----HHHHHTCCSCCHH
T ss_pred             cCCCCCcccCH----HHHHHhCCCCCHH
Confidence            4322 122223    4567777776543

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.63  E-value=0.12  Score=41.62  Aligned_cols=138  Identities=17%  Similarity=0.211  Sum_probs=71.3

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCC-hHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGG-LACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~   79 (192)
                      +|||.||+.++.+....|-   .++ .+........ ....++.+                +...-...+++|.+|+++.
T Consensus       254 TGKTlLAkAiA~e~~~~fi---~vs-~s~L~sk~vGesek~ir~l----------------F~~Ar~~aP~IIfiDEiDa  313 (467)
T 4b4t_H          254 TGKTLCARAVANRTDATFI---RVI-GSELVQKYVGEGARMVREL----------------FEMARTKKACIIFFDEIDA  313 (467)
T ss_dssp             SSHHHHHHHHHHHHTCEEE---EEE-GGGGCCCSSSHHHHHHHHH----------------HHHHHHTCSEEEEEECCTT
T ss_pred             CcHHHHHHHHHhccCCCeE---EEE-hHHhhcccCCHHHHHHHHH----------------HHHHHhcCCceEeeccccc
Confidence            6999999999998765542   222 2211111011 11111111                2222245689999999974


Q ss_pred             ch----------------hHHHhhccCCCC--CCCceEEEEecchhHHhh-----cCCCceEecCCCCHHHHHHHHHHhh
Q 039644           80 FS----------------QLESLMGSLDWL--TPVSRIILTTRNKQVLRN-----WGVSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus        80 ~~----------------~~~~l~~~~~~~--~~~~~iivTtR~~~~~~~-----~~~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      ..                ....+...+...  ..+..||.||........     ......+.++..+.++-.++|+.+.
T Consensus       314 i~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l  393 (467)
T 4b4t_H          314 VGGARFDDGAGGDNEVQRTMLELITQLDGFDPRGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHS  393 (467)
T ss_dssp             TSBCCSSSSCGGGGHHHHHHHHHHHHHHSSCCTTTEEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHH
T ss_pred             ccccccCcCCCccHHHHHHHHHHHHHhhccCCCCcEEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHHHHHHHHHh
Confidence            21                012222222222  233345556655432211     1235678888888888888887765


Q ss_pred             cCCC-CCCccHHHHHHHHHHHhCCCch
Q 039644          137 FKRN-HPDVGYEKLSSNVTKYAQGIPL  162 (192)
Q Consensus       137 ~~~~-~~~~~~~~~~~~i~~~~~g~Pl  162 (192)
                      ..-. ..+..+    ..+++.+.|+--
T Consensus       394 ~~~~l~~dvdl----~~LA~~T~GfSG  416 (467)
T 4b4t_H          394 KSMSVERGIRW----ELISRLCPNSTG  416 (467)
T ss_dssp             TTSCBCSSCCH----HHHHHHCCSCCH
T ss_pred             cCCCCCCCCCH----HHHHHHCCCCCH
Confidence            3322 112223    456777887643

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=95.61  E-value=0.016  Score=39.28  Aligned_cols=25  Identities=12%  Similarity=0.230  Sum_probs=17.5

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +|||||++.++......-...+++.
T Consensus        47 ~GKTtL~~~i~~~~~~~g~~~~~~~   71 (149)
T 2kjq_A           47 AGKSHLLQAWVAQALEAGKNAAYID   71 (149)
T ss_dssp             TTTCHHHHHHHHHHHTTTCCEEEEE
T ss_pred             CCHHHHHHHHHHHHHhcCCcEEEEc
Confidence            5999999999997654311256665

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=95.59  E-value=0.066  Score=40.39  Aligned_cols=17  Identities=24%  Similarity=0.364  Sum_probs=14.4

Q ss_pred             CchhHHHHHHHHHhhCC
Q 039644            1 IGKTAIARAIFDKISGD   17 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~   17 (192)
                      +|||+||+.+++.....
T Consensus        47 tGKT~la~aiA~~l~~~   63 (293)
T 3t15_A           47 QGKSFQCELVFRKMGIN   63 (293)
T ss_dssp             SCHHHHHHHHHHHHTCC
T ss_pred             CCHHHHHHHHHHHhCCC
Confidence            69999999999988543

>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=95.59  E-value=0.049  Score=44.30  Aligned_cols=98  Identities=15%  Similarity=0.181  Sum_probs=51.5

Q ss_pred             CCceEEEEEeCCCCc--------h-----hHHHhhccCCC--CCCCceEEEEecchhH-----HhhcCCCceEecCCCCH
Q 039644           66 SRMKVLIVFDDVTCF--------S-----QLESLMGSLDW--LTPVSRIILTTRNKQV-----LRNWGVSKIYEMEALEY  125 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~--------~-----~~~~l~~~~~~--~~~~~~iivTtR~~~~-----~~~~~~~~~~~l~~l~~  125 (192)
                      .+.+.+|+||+++..        .     ....+...+..  ...+..||.||.....     .........+.+...+.
T Consensus       295 ~~~p~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~v~vIaaTn~~~~Ld~al~r~gRf~~~i~i~~P~~  374 (489)
T 3hu3_A          295 KNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDA  374 (489)
T ss_dssp             HTCSEEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCTTSCEEEEEEESCGGGBCGGGGSTTSSCEEEECCCCCH
T ss_pred             hcCCcEEEecchhhhccccccccchHHHHHHHHHHHHhhccccCCceEEEEecCCccccCHHHhCCCcCceEEEeCCCCH
Confidence            456789999999421        1     11222222211  1234455556665422     11112345688999999


Q ss_pred             HHHHHHHHHhhcCCCC-CCccHHHHHHHHHHHhCCC-chHHHHH
Q 039644          126 HHALELFSQHAFKRNH-PDVGYEKLSSNVTKYAQGI-PLALKVL  167 (192)
Q Consensus       126 ~ea~~lf~~~~~~~~~-~~~~~~~~~~~i~~~~~g~-Plai~~~  167 (192)
                      ++-.+++......... .+..+    ..+.+.+.|+ +-.+..+
T Consensus       375 ~eR~~IL~~~~~~~~l~~~~~l----~~la~~t~g~s~~dL~~L  414 (489)
T 3hu3_A          375 TGRLEILQIHTKNMKLADDVDL----EQVANETHGHVGADLAAL  414 (489)
T ss_dssp             HHHHHHHHHHTTTSCBCTTCCH----HHHHHTCTTCCHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCcchhhH----HHHHHHccCCcHHHHHHH
Confidence            9999999877632221 12222    3455666665 4334433

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=95.17  E-value=0.62  Score=33.97  Aligned_cols=91  Identities=13%  Similarity=0.024  Sum_probs=45.4

Q ss_pred             CceEEEEecchhHHhh-c----CCCceEecCCCCHHHHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCC-CchHHHHHH-
Q 039644           96 VSRIILTTRNKQVLRN-W----GVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQG-IPLALKVLS-  168 (192)
Q Consensus        96 ~~~iivTtR~~~~~~~-~----~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g-~Plai~~~~-  168 (192)
                      +..||.||........ .    .....+.++..+.++-.+++.............   ....+...+.| .+--+..+. 
T Consensus       150 ~~~vI~~tn~~~~l~~~l~r~~rf~~~i~i~~P~~~~r~~il~~~~~~~~l~~~~---~~~~la~~~~G~~~~dl~~l~~  226 (257)
T 1lv7_A          150 GIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDI---DAAIIARGTPGFSGADLANLVN  226 (257)
T ss_dssp             CEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTC---CHHHHHHTCTTCCHHHHHHHHH
T ss_pred             CEEEEEeeCCchhCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhcCCCCccc---cHHHHHHHcCCCCHHHHHHHHH
Confidence            4456666655431111 1    124567788878888777776654222111111   12345666777 554443321 


Q ss_pred             -----HHhccC---CHHHHHHHHHHHHhc
Q 039644          169 -----CFLHKR---EKEVWESAIDKLQRI  189 (192)
Q Consensus       169 -----~~l~~~---~~~~w~~~l~~l~~~  189 (192)
                           +..++.   +.+.++.++++...+
T Consensus       227 ~a~~~a~~~~~~~i~~~~~~~a~~~~~~~  255 (257)
T 1lv7_A          227 EAALFAARGNKRVVSMVEFEKAKDKIMMG  255 (257)
T ss_dssp             HHHHHHHHTTCSSBCHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhCCCcccHHHHHHHHHHHhcC
Confidence                 111222   267777777766543

>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=95.16  E-value=0.51  Score=38.22  Aligned_cols=138  Identities=16%  Similarity=0.190  Sum_probs=69.0

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||+||+.++.+....|   +.++ .+...........               ......+.......+++|+||+++..
T Consensus        60 tGKT~Laraia~~~~~~f---~~is-~~~~~~~~~g~~~---------------~~~r~lf~~A~~~~p~ILfIDEid~l  120 (476)
T 2ce7_A           60 TGKTLLARAVAGEANVPF---FHIS-GSDFVELFVGVGA---------------ARVRDLFAQAKAHAPCIVFIDEIDAV  120 (476)
T ss_dssp             SSHHHHHHHHHHHHTCCE---EEEE-GGGTTTCCTTHHH---------------HHHHHHHHHHHHTCSEEEEEETGGGT
T ss_pred             CCHHHHHHHHHHHcCCCe---eeCC-HHHHHHHHhcccH---------------HHHHHHHHHHHhcCCCEEEEechhhh
Confidence            699999999999765433   2222 2221111000000               00111223333456899999999642


Q ss_pred             ----------------hhHHHhhccCCC--CCCCceEEEEecchhHHhh--c---CCCceEecCCCCHHHHHHHHHHhhc
Q 039644           81 ----------------SQLESLMGSLDW--LTPVSRIILTTRNKQVLRN--W---GVSKIYEMEALEYHHALELFSQHAF  137 (192)
Q Consensus        81 ----------------~~~~~l~~~~~~--~~~~~~iivTtR~~~~~~~--~---~~~~~~~l~~l~~~ea~~lf~~~~~  137 (192)
                                      .....+...+..  ...+..||.+|........  .   .....+.++..+.++-.+++..+..
T Consensus       121 ~~~r~~~~~g~~~~~~~~l~~LL~~ld~~~~~~~viVIaaTn~~~~Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~~~  200 (476)
T 2ce7_A          121 GRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTR  200 (476)
T ss_dssp             CCC---------CHHHHHHHHHHHHHHHSCGGGTEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHT
T ss_pred             hhhcccccCcCcHHHHHHHHHHHHHHhccCCCCCEEEEEecCChhhhchhhcccCcceeEeecCCCCHHHHHHHHHHHHH
Confidence                            012233222211  1234556667766543221  1   1234778888888777777776553


Q ss_pred             CCCC-CCccHHHHHHHHHHHhCCCc
Q 039644          138 KRNH-PDVGYEKLSSNVTKYAQGIP  161 (192)
Q Consensus       138 ~~~~-~~~~~~~~~~~i~~~~~g~P  161 (192)
                      .... ++..    ...+.+.+.|+.
T Consensus       201 ~~~l~~~v~----l~~la~~t~G~s  221 (476)
T 2ce7_A          201 NKPLAEDVN----LEIIAKRTPGFV  221 (476)
T ss_dssp             TSCBCTTCC----HHHHHHTCTTCC
T ss_pred             hCCCcchhh----HHHHHHhcCCCc
Confidence            2221 1111    234667777776

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=95.13  E-value=0.053  Score=44.67  Aligned_cols=21  Identities=19%  Similarity=0.314  Sum_probs=17.2

Q ss_pred             ceEecCCCCHHHHHHHHHHhh
Q 039644          116 KIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus       116 ~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      ..+.+.+++.++-..++..+.
T Consensus       246 ~vi~~~~~~~~e~~~Il~~~l  266 (543)
T 3m6a_A          246 EIINIAGYTEIEKLEIVKDHL  266 (543)
T ss_dssp             EEEECCCCCHHHHHHHHHHTH
T ss_pred             ceeeeCCCCHHHHHHHHHHHH
Confidence            578999999999888887654

>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=95.11  E-value=0.046  Score=40.34  Aligned_cols=70  Identities=13%  Similarity=0.301  Sum_probs=38.4

Q ss_pred             CceEEEEEeCCCCch-----------------hHHHhhccCCCCC---CCceEEEEecchhHHh--hc---CCCceEecC
Q 039644           67 RMKVLIVFDDVTCFS-----------------QLESLMGSLDWLT---PVSRIILTTRNKQVLR--NW---GVSKIYEME  121 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~-----------------~~~~l~~~~~~~~---~~~~iivTtR~~~~~~--~~---~~~~~~~l~  121 (192)
                      ..+.+|+||+++...                 ....+...+....   ....||.||.......  ..   .....+.++
T Consensus       102 ~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~ttn~~~~ld~~l~r~~Rf~~~i~i~  181 (268)
T 2r62_A          102 QAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVD  181 (268)
T ss_dssp             SCSCEEEESCGGGTTC----------CCCSCSSTTTTTTTTTCSSCSCSCCEEEECBSCCTTSCGGGGSSSSSCCCCBCC
T ss_pred             cCCeEEEEeChhhhcccccccccCCCchhHHHHHHHHHHHhhCcccCCCCEEEEEecCCchhcCHhHcCCCCCCeEEEec
Confidence            456899999996431                 1223333332211   2244666665543211  11   123457788


Q ss_pred             CCCHHHHHHHHHHhh
Q 039644          122 ALEYHHALELFSQHA  136 (192)
Q Consensus       122 ~l~~~ea~~lf~~~~  136 (192)
                      ..+.++-.+++....
T Consensus       182 ~p~~~~r~~il~~~~  196 (268)
T 2r62_A          182 KPDFNGRVEILKVHI  196 (268)
T ss_dssp             CCCTTTHHHHHHHHT
T ss_pred             CcCHHHHHHHHHHHH
Confidence            888888888887655

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=94.66  E-value=0.24  Score=37.02  Aligned_cols=19  Identities=16%  Similarity=0.142  Sum_probs=16.3

Q ss_pred             ceEecCCCCHHHHHHHHHH
Q 039644          116 KIYEMEALEYHHALELFSQ  134 (192)
Q Consensus       116 ~~~~l~~l~~~ea~~lf~~  134 (192)
                      ..+.+++++.++..+++..
T Consensus       195 ~~i~~~~~~~~~~~~il~~  213 (310)
T 1ofh_A          195 IRVELTALSAADFERILTE  213 (310)
T ss_dssp             EEEECCCCCHHHHHHHHHS
T ss_pred             ceEEcCCcCHHHHHHHHHh
Confidence            5699999999998888874

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=94.61  E-value=0.18  Score=43.22  Aligned_cols=115  Identities=21%  Similarity=0.250  Sum_probs=57.3

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||++|+.+++.....-...+.+. ++.........              ..  .....++.   ....+|+||+++..
T Consensus       532 tGKT~lA~ala~~l~~~~~~~i~i~-~s~~~~~~~~~--------------~~--~l~~~~~~---~~~~vl~lDEi~~~  591 (758)
T 3pxi_A          532 VGKTELARALAESIFGDEESMIRID-MSEYMEKHSTS--------------GG--QLTEKVRR---KPYSVVLLDAIEKA  591 (758)
T ss_dssp             SSHHHHHHHHHHHHHSCTTCEEEEE-GGGGCSSCCCC-------------------CHHHHHH---CSSSEEEEECGGGS
T ss_pred             CCHHHHHHHHHHHhcCCCcceEEEe-chhcccccccc--------------cc--hhhHHHHh---CCCeEEEEeCcccc
Confidence            6999999999997643323344454 33322220111              00  01111111   12348999999754


Q ss_pred             h--hHHHhhccC-----CC------CCCCceEEEEecchh---------HHhhc------CCCceEecCCCCHHHHHHHH
Q 039644           81 S--QLESLMGSL-----DW------LTPVSRIILTTRNKQ---------VLRNW------GVSKIYEMEALEYHHALELF  132 (192)
Q Consensus        81 ~--~~~~l~~~~-----~~------~~~~~~iivTtR~~~---------~~~~~------~~~~~~~l~~l~~~ea~~lf  132 (192)
                      .  ....+...+     ..      ...++.||.||....         +...+      .....+.+.+++.++...++
T Consensus       592 ~~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn~~~~~~~~~~~~~~~~f~p~l~~Rl~~~i~~~~l~~~~~~~i~  671 (758)
T 3pxi_A          592 HPDVFNILLQVLEDGRLTDSKGRTVDFRNTILIMTSNVGASEKDKVMGELKRAFRPEFINRIDEIIVFHSLEKKHLTEIV  671 (758)
T ss_dssp             CHHHHHHHHHHHHHSBCC-----CCBCTTCEEEEEESSSTTCCHHHHHHHHHHSCHHHHTTSSEEEECC--CHHHHHHHH
T ss_pred             CHHHHHHHHHHhccCeEEcCCCCEeccCCeEEEEeCCCChhhHHHHHHHHHhhCCHHHHhhCCeEEecCCCCHHHHHHHH
Confidence            3  233332211     11      123567888887311         01111      22358899999999888877


Q ss_pred             HHh
Q 039644          133 SQH  135 (192)
Q Consensus       133 ~~~  135 (192)
                      ...
T Consensus       672 ~~~  674 (758)
T 3pxi_A          672 SLM  674 (758)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.53  E-value=0.12  Score=41.30  Aligned_cols=139  Identities=18%  Similarity=0.199  Sum_probs=70.9

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCC-hHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGG-LACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~   79 (192)
                      +|||.||+.++......|-   .++ .+........ .....+.+                +...-...+++|.+|+++.
T Consensus       226 TGKTllAkAiA~e~~~~f~---~v~-~s~l~~~~vGese~~ir~l----------------F~~A~~~aP~IifiDEiDa  285 (434)
T 4b4t_M          226 TGKTLLARACAAQTNATFL---KLA-APQLVQMYIGEGAKLVRDA----------------FALAKEKAPTIIFIDELDA  285 (434)
T ss_dssp             SSHHHHHHHHHHHHTCEEE---EEE-GGGGCSSCSSHHHHHHHHH----------------HHHHHHHCSEEEEEECTHH
T ss_pred             CCHHHHHHHHHHHhCCCEE---EEe-hhhhhhcccchHHHHHHHH----------------HHHHHhcCCeEEeecchhh
Confidence            6999999999998765432   222 2221111011 11111111                1111134589999999962


Q ss_pred             c-------h-----h----HHHhhccCCCCC--CCceEEEEecchhHHhhc-----CCCceEecCCCCHHHHHHHHHHhh
Q 039644           80 F-------S-----Q----LESLMGSLDWLT--PVSRIILTTRNKQVLRNW-----GVSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus        80 ~-------~-----~----~~~l~~~~~~~~--~~~~iivTtR~~~~~~~~-----~~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      .       .     .    ...+...+....  .+--||.||.........     .....+.++..+.++-.++|..+.
T Consensus       286 l~~~R~~~~~~~~~~~~~~~~~lL~~ldg~~~~~~ViVIaaTNrp~~LD~AllRpGRfD~~I~i~lPd~~~R~~Il~~~~  365 (434)
T 4b4t_M          286 IGTKRFDSEKSGDREVQRTMLELLNQLDGFSSDDRVKVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHS  365 (434)
T ss_dssp             HHCCCSSGGGGTTHHHHHHHHHHHHHHTTSCSSCSSEEEEECSSCCCCCTTTCSTTSEEEEEECCCCCHHHHHHHHHHHH
T ss_pred             hhhccCCCCCCCchHHHHHHHHHHHHhhccCCCCCEEEEEeCCCchhcCHhHhcCCceeEEEEeCCcCHHHHHHHHHHHh
Confidence            1       0     1    223333333322  333455577655432221     124567888888888888887655


Q ss_pred             cCCC-CCCccHHHHHHHHHHHhCCCchH
Q 039644          137 FKRN-HPDVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       137 ~~~~-~~~~~~~~~~~~i~~~~~g~Pla  163 (192)
                      ..-. .++..+    ..+++.+.|+--|
T Consensus       366 ~~~~~~~dvdl----~~lA~~t~G~sGA  389 (434)
T 4b4t_M          366 RKMTTDDDINW----QELARSTDEFNGA  389 (434)
T ss_dssp             HHSCBCSCCCH----HHHHHHCSSCCHH
T ss_pred             cCCCCCCcCCH----HHHHHhCCCCCHH
Confidence            3222 122223    4567777776433

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.51  E-value=0.18  Score=40.20  Aligned_cols=163  Identities=17%  Similarity=0.202  Sum_probs=81.4

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCC-ChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPG-GLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~   79 (192)
                      +|||.||+.++......|-   .++ .+....... ......+.+                +...-...+++|.||+++.
T Consensus       227 TGKTlLAkAiA~e~~~~fi---~v~-~s~l~sk~vGesek~ir~l----------------F~~Ar~~aP~IIfiDEiDa  286 (437)
T 4b4t_I          227 TGKTLLAKAVANQTSATFL---RIV-GSELIQKYLGDGPRLCRQI----------------FKVAGENAPSIVFIDEIDA  286 (437)
T ss_dssp             TTHHHHHHHHHHHHTCEEE---EEE-SGGGCCSSSSHHHHHHHHH----------------HHHHHHTCSEEEEEEEESS
T ss_pred             chHHHHHHHHHHHhCCCEE---EEE-HHHhhhccCchHHHHHHHH----------------HHHHHhcCCcEEEEehhhh
Confidence            6999999999998765542   222 222111101 111111111                1112235689999999973


Q ss_pred             ch------------h----HHHhhccCCC--CCCCceEEEEecchhHHhhc--C---CCceEecCCCCHHHHHHHHHHhh
Q 039644           80 FS------------Q----LESLMGSLDW--LTPVSRIILTTRNKQVLRNW--G---VSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus        80 ~~------------~----~~~l~~~~~~--~~~~~~iivTtR~~~~~~~~--~---~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      ..            .    +..+...+..  ...+.-||.||.........  .   ....+.++.-+.++-.++|..+.
T Consensus       287 i~~~R~~~~~~~~~~~~~~l~~LL~~lDg~~~~~~ViVIaATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~~~l  366 (437)
T 4b4t_I          287 IGTKRYDSNSGGEREIQRTMLELLNQLDGFDDRGDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGIHT  366 (437)
T ss_dssp             SSCCCSCSSCSSCCHHHHHHHHHHHHHHHCCCSSSEEEEEEESCSTTCCTTSSCTTTEEEEECCCCCCHHHHHHHHHHHH
T ss_pred             hcccCCCCCCCccHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCChhhcCHHHhcCCceeEEEEcCCcCHHHHHHHHHHHh
Confidence            21            0    2223222221  22344566677665433222  1   23457788778888888887765


Q ss_pred             cCCC-CCCccHHHHHHHHHHHhCCCchH-HHHHH-----HHhccC-C---HHHHHHHHHHHH
Q 039644          137 FKRN-HPDVGYEKLSSNVTKYAQGIPLA-LKVLS-----CFLHKR-E---KEVWESAIDKLQ  187 (192)
Q Consensus       137 ~~~~-~~~~~~~~~~~~i~~~~~g~Pla-i~~~~-----~~l~~~-~---~~~w~~~l~~l~  187 (192)
                      ..-. ..+..+    ..+++.+.|+--| |..+.     ..++.. .   .+..+.+++++.
T Consensus       367 ~~~~l~~dvdl----~~LA~~T~GfSGADI~~l~~eA~~~Air~~~~~It~eDf~~Al~rv~  424 (437)
T 4b4t_I          367 SKMNLSEDVNL----ETLVTTKDDLSGADIQAMCTEAGLLALRERRMQVTAEDFKQAKERVM  424 (437)
T ss_dssp             TTSCBCSCCCH----HHHHHHCCSCCHHHHHHHHHHHHHHHHHTTCSCBCHHHHHHHHHHHH
T ss_pred             cCCCCCCcCCH----HHHHHhCCCCCHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHHh
Confidence            3322 122233    4566777776433 22221     122322 1   566666666554

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=94.48  E-value=0.078  Score=35.39  Aligned_cols=36  Identities=14%  Similarity=-0.009  Sum_probs=21.6

Q ss_pred             EEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecc
Q 039644           70 VLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRN  105 (192)
Q Consensus        70 ~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~  105 (192)
                      ..|+||+++...  ....+...+.......++|.||..
T Consensus        78 g~l~ldei~~l~~~~q~~Ll~~l~~~~~~~~~I~~t~~  115 (145)
T 3n70_A           78 GTLVLSHPEHLTREQQYHLVQLQSQEHRPFRLIGIGDT  115 (145)
T ss_dssp             SCEEEECGGGSCHHHHHHHHHHHHSSSCSSCEEEEESS
T ss_pred             cEEEEcChHHCCHHHHHHHHHHHhhcCCCEEEEEECCc
Confidence            468999998553  233444333333445678888764

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.46  E-value=0.14  Score=40.83  Aligned_cols=18  Identities=28%  Similarity=0.534  Sum_probs=15.2

Q ss_pred             CchhHHHHHHHHHhhCCC
Q 039644            1 IGKTAIARAIFDKISGDF   18 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F   18 (192)
                      +|||.||+.+++.....|
T Consensus       217 tGKT~lakAiA~~~~~~~  234 (428)
T 4b4t_K          217 TGKTMLVKAVANSTKAAF  234 (428)
T ss_dssp             TTHHHHHHHHHHHHTCEE
T ss_pred             CCHHHHHHHHHHHhCCCe
Confidence            699999999999876544

>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=94.37  E-value=0.22  Score=43.02  Aligned_cols=137  Identities=16%  Similarity=0.162  Sum_probs=70.3

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC--cC-chHHHHhhcCCceEEEEEeCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV--MP-YIDLNFRRLSRMKVLIVFDDV   77 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--~~-~~~~l~~~l~~~~~LlVlDdv   77 (192)
                      +|||+||+.++.+...+|   +.++ .+          ++.        .....  .. +...+.......+++|+||++
T Consensus       249 TGKT~LAraiA~elg~~~---~~v~-~~----------~l~--------sk~~gese~~lr~lF~~A~~~~PsIIfIDEi  306 (806)
T 3cf2_A          249 TGKTLIARAVANETGAFF---FLIN-GP----------EIM--------SKLAGESESNLRKAFEEAEKNAPAIIFIDEL  306 (806)
T ss_dssp             SCHHHHHHHHHTTTTCEE---EEEE-HH----------HHH--------SSCTTHHHHHHHHHHHHHTTSCSEEEEEESG
T ss_pred             CCHHHHHHHHHHHhCCeE---EEEE-hH----------Hhh--------cccchHHHHHHHHHHHHHHHcCCeEEEEehh
Confidence            699999999999876543   2332 11          111        11111  01 222233333567899999999


Q ss_pred             CCch--------h-----HHHhhccCCCC--CCCceEEEEecchhHHhhc-----CCCceEecCCCCHHHHHHHHHHhhc
Q 039644           78 TCFS--------Q-----LESLMGSLDWL--TPVSRIILTTRNKQVLRNW-----GVSKIYEMEALEYHHALELFSQHAF  137 (192)
Q Consensus        78 ~~~~--------~-----~~~l~~~~~~~--~~~~~iivTtR~~~~~~~~-----~~~~~~~l~~l~~~ea~~lf~~~~~  137 (192)
                      +...        .     ...+...+...  ..+.-||-+|.........     .....+.++..+..+-.++|..+..
T Consensus       307 Dal~~~r~~~~~~~~~riv~~LL~~mdg~~~~~~V~VIaaTN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~  386 (806)
T 3cf2_A          307 DAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTK  386 (806)
T ss_dssp             GGTCCTTTTCCCTTHHHHHHHHHTHHHHCCGGGCEEEEEECSSTTTSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCS
T ss_pred             cccccccCCCCChHHHHHHHHHHHHHhcccccCCEEEEEecCChhhcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhc
Confidence            7421        1     12222222111  1233344455544322111     1245788888888888888877653


Q ss_pred             CCC-CCCccHHHHHHHHHHHhCCCchH
Q 039644          138 KRN-HPDVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       138 ~~~-~~~~~~~~~~~~i~~~~~g~Pla  163 (192)
                      ... ..+..    ...+++.+.|+--|
T Consensus       387 ~~~~~~dvd----l~~lA~~T~Gfsga  409 (806)
T 3cf2_A          387 NMKLADDVD----LEQVANETHGHVGA  409 (806)
T ss_dssp             SSEECTTCC----HHHHHHHCCSCCHH
T ss_pred             CCCCCcccC----HHHHHHhcCCCCHH
Confidence            221 11222    34567777777543

>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=94.35  E-value=0.31  Score=35.79  Aligned_cols=15  Identities=33%  Similarity=0.262  Sum_probs=12.9

Q ss_pred             CchhHHHHHHHHHhh
Q 039644            1 IGKTAIARAIFDKIS   15 (192)
Q Consensus         1 iGKTtLa~~~~~~~~   15 (192)
                      +|||++|+.+++...
T Consensus        40 tGKt~la~~i~~~~~   54 (265)
T 2bjv_A           40 TGKELIASRLHYLSS   54 (265)
T ss_dssp             SCHHHHHHHHHHTST
T ss_pred             CcHHHHHHHHHHhcC
Confidence            699999999998654

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=94.10  E-value=0.23  Score=43.13  Aligned_cols=67  Identities=10%  Similarity=0.061  Sum_probs=34.4

Q ss_pred             CceEEEEEeCCCCch---------h-HHHhhccCCCCCCCceEEEEecchhHHhh-----c-CCCceEecCCCCHHHHHH
Q 039644           67 RMKVLIVFDDVTCFS---------Q-LESLMGSLDWLTPVSRIILTTRNKQVLRN-----W-GVSKIYEMEALEYHHALE  130 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~---------~-~~~l~~~~~~~~~~~~iivTtR~~~~~~~-----~-~~~~~~~l~~l~~~ea~~  130 (192)
                      +.+.+|+||+++...         + ...+...+.  ..+..+|.+|........     . .....+.+++.+.++..+
T Consensus       262 ~~~~iL~IDEi~~l~~~~~~~g~~~~~~~L~~~l~--~~~i~~I~at~~~~~~~~~~d~aL~rRf~~i~l~~p~~~e~~~  339 (854)
T 1qvr_A          262 QGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALA--RGELRLIGATTLDEYREIEKDPALERRFQPVYVDEPTVEETIS  339 (854)
T ss_dssp             CSSEEEEECCC-------------------HHHHH--TTCCCEEEEECHHHHHHHTTCTTTCSCCCCEEECCCCHHHHHH
T ss_pred             CCCeEEEEecHHHHhccCCccchHHHHHHHHHHHh--CCCeEEEEecCchHHhhhccCHHHHhCCceEEeCCCCHHHHHH
Confidence            367899999997542         1 112222221  123345555544332111     1 223458899999999998


Q ss_pred             HHHHh
Q 039644          131 LFSQH  135 (192)
Q Consensus       131 lf~~~  135 (192)
                      ++...
T Consensus       340 iL~~~  344 (854)
T 1qvr_A          340 ILRGL  344 (854)
T ss_dssp             HHHHH
T ss_pred             HHHhh
Confidence            88643

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=93.93  E-value=0.9  Score=33.76  Aligned_cols=116  Identities=16%  Similarity=0.161  Sum_probs=59.2

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhc-CCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRL-SRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l-~~~~~LlVlDdv~~   79 (192)
                      +||||||+.++.....   ..+.+. ..+....  ...+..+              .+..+.... ...++++++|+++.
T Consensus        55 tGKTtLakala~~~~~---~~i~i~-g~~l~~~--~~~~~~~--------------~i~~vf~~a~~~~p~i~~~Deid~  114 (274)
T 2x8a_A           55 CGKTLLAKAVANESGL---NFISVK-GPELLNM--YVGESER--------------AVRQVFQRAKNSAPCVIFFDEVDA  114 (274)
T ss_dssp             SCHHHHHHHHHHHTTC---EEEEEE-TTTTCSS--TTHHHHH--------------HHHHHHHHHHHTCSEEEEEETCTT
T ss_pred             CcHHHHHHHHHHHcCC---CEEEEE-cHHHHhh--hhhHHHH--------------HHHHHHHHHHhcCCCeEeeehhhh
Confidence            6999999999997643   234444 2221111  1111111              111112221 23578999999974


Q ss_pred             ch-------------hHHHhhccCCCCC--CCceEEEEecchhHHhhc-----CCCceEecCCCCHHHHHHHHHHhh
Q 039644           80 FS-------------QLESLMGSLDWLT--PVSRIILTTRNKQVLRNW-----GVSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus        80 ~~-------------~~~~l~~~~~~~~--~~~~iivTtR~~~~~~~~-----~~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      ..             ....+...+....  ...-++.+|.........     .....+.++..+.++-.+++....
T Consensus       115 ~~~~r~~~~~~~~~~~~~~~l~~Lsgg~~~~~~i~ia~tn~p~~LD~al~r~gRfd~~i~~~~P~~~~r~~il~~~~  191 (274)
T 2x8a_A          115 LCPRRSDRETGASVRVVNQLLTEMDGLEARQQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTIT  191 (274)
T ss_dssp             TCC---------CTTHHHHHHHHHHTCCSTTCEEEEEEESCGGGSCHHHHSTTSSCEEEECCSCCHHHHHHHHHHHT
T ss_pred             hhcccCCCcchHHHHHHHHHHHhhhcccccCCEEEEeecCChhhCCHhhcCcccCCeEEEeCCcCHHHHHHHHHHHH
Confidence            21             1122222222211  223344466655433221     235667888888888888887765

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=93.47  E-value=0.053  Score=37.21  Aligned_cols=16  Identities=44%  Similarity=0.515  Sum_probs=13.6

Q ss_pred             CchhHHHHHHHHHhhC
Q 039644            1 IGKTAIARAIFDKISG   16 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~   16 (192)
                      +|||+||+.+++....
T Consensus        54 ~GKT~la~~~~~~~~~   69 (187)
T 2p65_A           54 VGKTAIVEGLAIKIVQ   69 (187)
T ss_dssp             GCHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHh
Confidence            5999999999997643

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=92.79  E-value=1.1  Score=33.92  Aligned_cols=14  Identities=36%  Similarity=0.437  Sum_probs=12.3

Q ss_pred             CchhHHHHHHHHHh
Q 039644            1 IGKTAIARAIFDKI   14 (192)
Q Consensus         1 iGKTtLa~~~~~~~   14 (192)
                      +|||++|+.+++..
T Consensus        36 tGKt~lAr~i~~~~   49 (304)
T 1ojl_A           36 TGKELVARALHACS   49 (304)
T ss_dssp             SCHHHHHHHHHHHS
T ss_pred             chHHHHHHHHHHhC
Confidence            69999999999864

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=92.25  E-value=1.1  Score=36.44  Aligned_cols=69  Identities=13%  Similarity=0.270  Sum_probs=38.0

Q ss_pred             ceEEEEEeCCCCc------------hh----HHHhhccCCCCC--CCceEEEEecchhHHhhc-----CCCceEecCCCC
Q 039644           68 MKVLIVFDDVTCF------------SQ----LESLMGSLDWLT--PVSRIILTTRNKQVLRNW-----GVSKIYEMEALE  124 (192)
Q Consensus        68 ~~~LlVlDdv~~~------------~~----~~~l~~~~~~~~--~~~~iivTtR~~~~~~~~-----~~~~~~~l~~l~  124 (192)
                      .++++++|+++..            ..    ...+...+....  .+..++.+|.........     .....+.++..+
T Consensus       123 ~p~il~IDEId~l~~~r~~~~~~~~~e~~~~l~~LL~~Ldg~~~~~~viviAatn~p~~LD~aLlr~gRfdr~i~i~~Pd  202 (499)
T 2dhr_A          123 APCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPD  202 (499)
T ss_dssp             SSCEEEEECGGGTCCCSSSSTTTSSHHHHHHHHHHHHHGGGCCSSCCCEEEECCSCGGGSCTTTSSTTSSCCEEECCCCC
T ss_pred             CCCEEEEehHHHHHHhhccCcCCCcHHHHHHHHHHHHHhcccccCccEEEEEecCChhhcCcccccccccceEEecCCCC
Confidence            4689999999532            11    233333332222  233344455555432211     124578888888


Q ss_pred             HHHHHHHHHHhh
Q 039644          125 YHHALELFSQHA  136 (192)
Q Consensus       125 ~~ea~~lf~~~~  136 (192)
                      .++-.+++..+.
T Consensus       203 ~~~R~~IL~~~~  214 (499)
T 2dhr_A          203 VKGREQILRIHA  214 (499)
T ss_dssp             HHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHH
Confidence            888888887665

>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=92.16  E-value=1.2  Score=32.26  Aligned_cols=43  Identities=16%  Similarity=0.199  Sum_probs=25.4

Q ss_pred             CceEecCCCCHHHHHHHHHHhhcCCCC-CCccHHHHHHHHHHHhCCCc
Q 039644          115 SKIYEMEALEYHHALELFSQHAFKRNH-PDVGYEKLSSNVTKYAQGIP  161 (192)
Q Consensus       115 ~~~~~l~~l~~~ea~~lf~~~~~~~~~-~~~~~~~~~~~i~~~~~g~P  161 (192)
                      ...+.++..+.++-.+++......... .+..    ...+.+.+.|.-
T Consensus       178 ~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~----~~~la~~~~G~~  221 (254)
T 1ixz_A          178 DRQIAIDAPDVKGREQILRIHARGKPLAEDVD----LALLAKRTPGFV  221 (254)
T ss_dssp             CEEEECCSCCHHHHHHHHHHHHTTSCBCTTCC----HHHHHHTCTTCC
T ss_pred             CeEEeeCCcCHHHHHHHHHHHHcCCCCCcccC----HHHHHHHcCCCC
Confidence            456888888888888888765522211 1111    234666676654

>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=92.02  E-value=1.5  Score=37.42  Aligned_cols=69  Identities=9%  Similarity=0.139  Sum_probs=39.0

Q ss_pred             CceEEEEEeCCCCc----------hhHHHhhccCCCCCCCceEEEEecchhHHhhc-------CCCceEecCCCCHHHHH
Q 039644           67 RMKVLIVFDDVTCF----------SQLESLMGSLDWLTPVSRIILTTRNKQVLRNW-------GVSKIYEMEALEYHHAL  129 (192)
Q Consensus        67 ~~~~LlVlDdv~~~----------~~~~~l~~~~~~~~~~~~iivTtR~~~~~~~~-------~~~~~~~l~~l~~~ea~  129 (192)
                      ..+.+|++|+++..          .+...+...+.. ..+..+|.+|.........       ..-..+.+...+.++..
T Consensus       277 ~~~~iL~IDEi~~l~~~~~~~~~~~~~~~~L~~~l~-~~~~~~I~at~~~~~~~~~~~d~aL~~Rf~~i~v~~p~~~e~~  355 (758)
T 1r6b_X          277 DTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLS-SGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETV  355 (758)
T ss_dssp             SSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSS-SCCCEEEEEECHHHHHCCCCCTTSSGGGEEEEECCCCCHHHHH
T ss_pred             cCCeEEEEechHHHhhcCCCCcchHHHHHHHHHHHh-CCCeEEEEEeCchHHhhhhhcCHHHHhCceEEEcCCCCHHHHH
Confidence            35789999999854          112222222222 2345566666543321111       11236889999999988


Q ss_pred             HHHHHhh
Q 039644          130 ELFSQHA  136 (192)
Q Consensus       130 ~lf~~~~  136 (192)
                      +++....
T Consensus       356 ~il~~l~  362 (758)
T 1r6b_X          356 QIINGLK  362 (758)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8877543

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=91.83  E-value=1.3  Score=32.67  Aligned_cols=44  Identities=16%  Similarity=0.195  Sum_probs=26.2

Q ss_pred             CCceEecCCCCHHHHHHHHHHhhcCCCC-CCccHHHHHHHHHHHhCCCc
Q 039644          114 VSKIYEMEALEYHHALELFSQHAFKRNH-PDVGYEKLSSNVTKYAQGIP  161 (192)
Q Consensus       114 ~~~~~~l~~l~~~ea~~lf~~~~~~~~~-~~~~~~~~~~~i~~~~~g~P  161 (192)
                      ....+.++..+.++-.+++....-.... ++..    ...+...+.|..
T Consensus       201 f~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~----~~~la~~~~G~~  245 (278)
T 1iy2_A          201 FDRQIAIDAPDVKGREQILRIHARGKPLAEDVD----LALLAKRTPGFV  245 (278)
T ss_dssp             SCCEEECCCCCHHHHHHHHHHHHTTSCBCTTCC----HHHHHHTCTTCC
T ss_pred             CCeEEEeCCcCHHHHHHHHHHHHccCCCCcccC----HHHHHHHcCCCC
Confidence            3457888888888888888765522211 1111    234666677765

>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=91.73  E-value=0.79  Score=32.25  Aligned_cols=22  Identities=18%  Similarity=0.075  Sum_probs=16.5

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +|||||+..++.  . .-..++|++
T Consensus        31 sGKTtl~~~l~~--~-~~~~v~~i~   52 (220)
T 2cvh_A           31 SGKTTLALQTGL--L-SGKKVAYVD   52 (220)
T ss_dssp             SSHHHHHHHHHH--H-HCSEEEEEE
T ss_pred             CCHHHHHHHHHH--H-cCCcEEEEE
Confidence            699999999998  2 224567776

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=91.43  E-value=0.12  Score=39.22  Aligned_cols=25  Identities=24%  Similarity=0.309  Sum_probs=17.8

Q ss_pred             CchhHHHHHHHHHhh-CCCcceEEEe
Q 039644            1 IGKTAIARAIFDKIS-GDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~-~~F~~~~wv~   25 (192)
                      +|||+||..+++... ..-..+.++.
T Consensus       163 tGKT~La~aia~~~~~~~g~~v~~~~  188 (308)
T 2qgz_A          163 IGKSYLLAAMAHELSEKKGVSTTLLH  188 (308)
T ss_dssp             SSHHHHHHHHHHHHHHHSCCCEEEEE
T ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEEE
Confidence            699999999999765 4433444553

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=91.36  E-value=1.1  Score=36.12  Aligned_cols=66  Identities=9%  Similarity=0.066  Sum_probs=34.5

Q ss_pred             CceEEEEEeCCCCchhHHHhhccCCCCCCCceEEEEecchhHHh---h----cCCCceEecCCCCHHHHHHHHHHhh
Q 039644           67 RMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLR---N----WGVSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~~~~~l~~~~~~~~~~~~iivTtR~~~~~~---~----~~~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      ..+.+|++|  -.......+...+.  .+..++|.+|.......   .    ...-..+.+++.+.++..+++....
T Consensus       266 ~~~~iLfiD--~~~~a~~~L~~~L~--~g~v~vI~at~~~e~~~~~~~~~al~~Rf~~i~v~~p~~e~~~~iL~~~~  338 (468)
T 3pxg_A          266 AGNIILFID--AAIDASNILKPSLA--RGELQCIGATTLDEYRKYIEKDAALERRFQPIQVDQPSVDESIQILQGLR  338 (468)
T ss_dssp             CCCCEEEEC--C--------CCCTT--SSSCEEEEECCTTTTHHHHTTCSHHHHSEEEEECCCCCHHHHHHHHHHTT
T ss_pred             cCCeEEEEe--CchhHHHHHHHhhc--CCCEEEEecCCHHHHHHHhhcCHHHHHhCccceeCCCCHHHHHHHHHHHH
Confidence            567889999  22222233433332  12345555554433111   0    0123468999999999999998654

>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=91.14  E-value=4  Score=31.03  Aligned_cols=98  Identities=12%  Similarity=-0.049  Sum_probs=62.8

Q ss_pred             CceEEEEEeCCCC-c--hhHHHhhccCCCCCCCceEEEEecc-------hhHHhhc-CCCceEecCCCCHHHHHHHHHHh
Q 039644           67 RMKVLIVFDDVTC-F--SQLESLMGSLDWLTPVSRIILTTRN-------KQVLRNW-GVSKIYEMEALEYHHALELFSQH  135 (192)
Q Consensus        67 ~~~~LlVlDdv~~-~--~~~~~l~~~~~~~~~~~~iivTtR~-------~~~~~~~-~~~~~~~l~~l~~~ea~~lf~~~  135 (192)
                      +.+-++|+|+++. .  ..++.+...+.+..+++.+|+++..       ..+.... +....++..+++..+....+...
T Consensus        75 ~~~kvvii~~~~~kl~~~~~~aLl~~le~p~~~~~~il~~~~~~~~~~~~k~~~~i~sr~~~~~~~~l~~~~l~~~l~~~  154 (343)
T 1jr3_D           75 ASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAAR  154 (343)
T ss_dssp             CSCEEEEEECCSSCCCTTHHHHHHHHHTTCBTTEEEEEEESCCCTTTTTSHHHHHHTTTCEEEEECCCCTTHHHHHHHHH
T ss_pred             cCCeEEEEECCCCCCChHHHHHHHHHHhcCCCCeEEEEEcCCCChhhHhhHHHHHHHhCceEEEeeCCCHHHHHHHHHHH
Confidence            4566889999875 3  4567776666655567777777643       1233332 45678999999999888777665


Q ss_pred             hcCCCCCCccHHHHHHHHHHHhCCCchHHHH
Q 039644          136 AFKRNHPDVGYEKLSSNVTKYAQGIPLALKV  166 (192)
Q Consensus       136 ~~~~~~~~~~~~~~~~~i~~~~~g~Plai~~  166 (192)
                      +-...  -.-..+.+..+++.++|.+.++..
T Consensus       155 ~~~~g--~~i~~~a~~~l~~~~~gdl~~~~~  183 (343)
T 1jr3_D          155 AKQLN--LELDDAANQVLCYCYEGNLLALAQ  183 (343)
T ss_dssp             HHHTT--CEECHHHHHHHHHSSTTCHHHHHH
T ss_pred             HHHcC--CCCCHHHHHHHHHHhchHHHHHHH
Confidence            53221  122345566777778887776554

>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=89.70  E-value=1.2  Score=38.61  Aligned_cols=16  Identities=25%  Similarity=0.507  Sum_probs=13.5

Q ss_pred             CchhHHHHHHHHHhhC
Q 039644            1 IGKTAIARAIFDKISG   16 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~   16 (192)
                      +|||++|+.+++....
T Consensus       599 tGKT~lA~~la~~~~~  614 (854)
T 1qvr_A          599 VGKTELAKTLAATLFD  614 (854)
T ss_dssp             SSHHHHHHHHHHHHHS
T ss_pred             CCHHHHHHHHHHHhcC
Confidence            6999999999997643

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=89.70  E-value=0.088  Score=36.86  Aligned_cols=43  Identities=12%  Similarity=0.042  Sum_probs=24.2

Q ss_pred             HHhhcCCceEEEEEeCCCCc-hhHHHhhccCCCCCCCceEEEEecc
Q 039644           61 NFRRLSRMKVLIVFDDVTCF-SQLESLMGSLDWLTPVSRIILTTRN  105 (192)
Q Consensus        61 l~~~l~~~~~LlVlDdv~~~-~~~~~l~~~~~~~~~~~~iivTtR~  105 (192)
                      +...+.+..-+|++|.+... .+|......+.+  .+..|++|.+.
T Consensus        69 ~~~~~~~~~dvviIDE~Q~~~~~~~~~l~~l~~--~~~~Vi~~Gl~  112 (184)
T 2orw_A           69 MRKYIEEDTRGVFIDEVQFFNPSLFEVVKDLLD--RGIDVFCAGLD  112 (184)
T ss_dssp             GGGGCCTTEEEEEECCGGGSCTTHHHHHHHHHH--TTCEEEEEEES
T ss_pred             HHHHhcCCCCEEEEECcccCCHHHHHHHHHHHH--CCCCEEEEeec
Confidence            33444445669999998754 233333222221  26778888774

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=89.67  E-value=0.13  Score=34.13  Aligned_cols=36  Identities=11%  Similarity=0.073  Sum_probs=19.9

Q ss_pred             EEEEEeCCCCch--hHHHhhccCCCC-CCCceEEEEecc
Q 039644           70 VLIVFDDVTCFS--QLESLMGSLDWL-TPVSRIILTTRN  105 (192)
Q Consensus        70 ~LlVlDdv~~~~--~~~~l~~~~~~~-~~~~~iivTtR~  105 (192)
                      -.++||+++...  ....+...+... ..+.++|.||..
T Consensus        77 ~~l~lDei~~l~~~~q~~Ll~~l~~~~~~~~~iI~~tn~  115 (143)
T 3co5_A           77 GVLYVGDIAQYSRNIQTGITFIIGKAERCRVRVIASCSY  115 (143)
T ss_dssp             SEEEEEECTTCCHHHHHHHHHHHHHHTTTTCEEEEEEEE
T ss_pred             CeEEEeChHHCCHHHHHHHHHHHHhCCCCCEEEEEecCC
Confidence            478999998653  223333222211 345678887753

>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=89.50  E-value=0.46  Score=38.39  Aligned_cols=24  Identities=25%  Similarity=0.512  Sum_probs=16.8

Q ss_pred             CchhHHHHHHHHHhhCCCc-ceEEE
Q 039644            1 IGKTAIARAIFDKISGDFE-CSCFL   24 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~-~~~wv   24 (192)
                      +|||||+..+.......+. ..++.
T Consensus       162 vGKTtL~~~l~~~~~~~~~~i~V~~  186 (473)
T 1sky_E          162 VGKTVLIQELIHNIAQEHGGISVFA  186 (473)
T ss_dssp             SCHHHHHHHHHHHHHHHTCCCEEEE
T ss_pred             CCccHHHHHHHhhhhhccCcEEEEe
Confidence            6999999999987654443 33443

>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=89.06  E-value=0.1  Score=40.09  Aligned_cols=22  Identities=18%  Similarity=0.083  Sum_probs=16.0

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +|||+||.+++..   .-..+.|++
T Consensus       134 sGKTtLAlqlA~~---~G~~VlyIs  155 (331)
T 2vhj_A          134 SGKTPLVHALGEA---LGGKDKYAT  155 (331)
T ss_dssp             SSHHHHHHHHHHH---HHTTSCCEE
T ss_pred             CCHHHHHHHHHHh---CCCCEEEEE
Confidence            6999999999886   112346666

>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=88.65  E-value=0.59  Score=39.95  Aligned_cols=21  Identities=10%  Similarity=0.098  Sum_probs=15.8

Q ss_pred             ceEecCCCCHHHHHHHHHHhh
Q 039644          116 KIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus       116 ~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      ..+.+.+++.++...++....
T Consensus       646 ~~i~~~~l~~~~~~~i~~~~l  666 (758)
T 1r6b_X          646 NIIWFDHLSTDVIHQVVDKFI  666 (758)
T ss_dssp             EEEECCCCCHHHHHHHHHHHH
T ss_pred             cceeeCCCCHHHHHHHHHHHH
Confidence            568889999888777776543

>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=87.66  E-value=0.18  Score=39.92  Aligned_cols=18  Identities=28%  Similarity=0.362  Sum_probs=14.3

Q ss_pred             CchhHHHHHHHHHhhCCC
Q 039644            1 IGKTAIARAIFDKISGDF   18 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F   18 (192)
                      +|||||+..+++.+.+..
T Consensus       185 ~GKTtLl~~Iar~i~~~~  202 (422)
T 3ice_A          185 AGKTMLLQNIAQSIAYNH  202 (422)
T ss_dssp             SSHHHHHHHHHHHHHHHC
T ss_pred             CChhHHHHHHHHHHhhcC
Confidence            599999999998765433

>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=87.16  E-value=1.6  Score=35.28  Aligned_cols=43  Identities=19%  Similarity=0.284  Sum_probs=26.5

Q ss_pred             CchhHHHHHHHHHhh-CCCcceEEEeeccccccCCCChHHHHHHHHHH
Q 039644            1 IGKTAIARAIFDKIS-GDFECSCFLENVREESQRPGGLACLRQKLLSN   47 (192)
Q Consensus         1 iGKTtLa~~~~~~~~-~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~   47 (192)
                      +|||+|+.+++..+. .+-+.++++- +++.   +....+++..+...
T Consensus       164 ~GKT~L~~~i~~~~~~~~~~v~V~~~-iGER---~rEv~e~~~~~~~~  207 (482)
T 2ck3_D          164 VGKTVLIMELINNVAKAHGGYSVFAG-VGER---TREGNDLYHEMIES  207 (482)
T ss_dssp             SSHHHHHHHHHHHTTTTCSSEEEEEE-ESCC---HHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHhhHhhCCCEEEEEE-CCCc---chHHHHHHHHhhhc
Confidence            699999999999763 3334455543 3331   13466666666543

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=86.87  E-value=2.8  Score=35.81  Aligned_cols=67  Identities=9%  Similarity=0.067  Sum_probs=35.6

Q ss_pred             CCceEEEEEeCCCCchhHHHhhccCCCCCCCceEEEEecchhHHhhc-------CCCceEecCCCCHHHHHHHHHHhh
Q 039644           66 SRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNW-------GVSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~~~~~~l~~~~~~~~~~~~iivTtR~~~~~~~~-------~~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      ...+.+|++|  ........+...+.  ....++|.+|.........       ..-..+.++..+.++..+++....
T Consensus       265 ~~~~~iLfiD--~~~~~~~~L~~~l~--~~~v~~I~at~~~~~~~~~~~d~al~rRf~~i~v~~p~~~~~~~il~~~~  338 (758)
T 3pxi_A          265 QAGNIILFID--AAIDASNILKPSLA--RGELQCIGATTLDEYRKYIEKDAALERRFQPIQVDQPSVDESIQILQGLR  338 (758)
T ss_dssp             TCCCCEEEEC--C--------CCCTT--SSSCEEEEECCTTTTHHHHTTCSHHHHSEEEEECCCCCHHHHHHHHHHTT
T ss_pred             hcCCEEEEEc--CchhHHHHHHHHHh--cCCEEEEeCCChHHHHHHhhccHHHHhhCcEEEeCCCCHHHHHHHHHHHH
Confidence            4567899999  22222233333332  2334566655443311100       122568999999999999998654

>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=85.77  E-value=2.3  Score=32.68  Aligned_cols=25  Identities=16%  Similarity=0.147  Sum_probs=18.3

Q ss_pred             CchhHHHHHHHHHhhC------CCcceEEEe
Q 039644            1 IGKTAIARAIFDKISG------DFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~------~F~~~~wv~   25 (192)
                      +|||+||.+++.....      .-..++|++
T Consensus       133 sGKTtla~~la~~~~~~~~~gg~~~~vlyi~  163 (343)
T 1v5w_A          133 TGKTQLSHTLCVTAQLPGAGGYPGGKIIFID  163 (343)
T ss_dssp             CTHHHHHHHHHHHTTSCBTTTBCCCEEEEEE
T ss_pred             CCHHHHHHHHHHHHhcccccCCCCCeEEEEE
Confidence            6999999999986432      224677887

>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=85.60  E-value=1.9  Score=35.04  Aligned_cols=42  Identities=21%  Similarity=0.214  Sum_probs=27.4

Q ss_pred             CchhHHHHHHHHHhh-CCCcceEEEeeccccccCCCChHHHHHHHHH
Q 039644            1 IGKTAIARAIFDKIS-GDFECSCFLENVREESQRPGGLACLRQKLLS   46 (192)
Q Consensus         1 iGKTtLa~~~~~~~~-~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~   46 (192)
                      +|||+|+.++++.+. .+-+.++++- +++-   .....+++.++..
T Consensus       176 vGKT~L~~~l~~~~a~~~~~v~V~~~-iGER---~rEv~e~~~~~~~  218 (498)
T 1fx0_B          176 VGKTVLIMELINNIAKAHGGVSVFGG-VGER---TREGNDLYMEMKE  218 (498)
T ss_dssp             SSHHHHHHHHHHHTTTTCSSCEEEEE-ESCC---SHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHHhhCCCEEEEEE-cccC---cHHHHHHHHhhhc
Confidence            699999999999764 4445566664 4331   1356677766654

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=84.89  E-value=2.3  Score=29.89  Aligned_cols=25  Identities=8%  Similarity=0.003  Sum_probs=18.8

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +||||.++.+++.++.+...++...
T Consensus        11 sGKsTq~~~L~~~L~~~g~~v~~tr   35 (197)
T 3hjn_A           11 SGKSTQIQLLAQYLEKRGKKVILKR   35 (197)
T ss_dssp             SSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCHHHHHHHHHHHHHHCCCcEEEEE
Confidence            6999999999998876544444443

>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=84.39  E-value=0.44  Score=32.47  Aligned_cols=15  Identities=27%  Similarity=0.501  Sum_probs=13.4

Q ss_pred             CchhHHHHHHHHHhh
Q 039644            1 IGKTAIARAIFDKIS   15 (192)
Q Consensus         1 iGKTtLa~~~~~~~~   15 (192)
                      +||||+|+.+..++.
T Consensus        14 sGKST~a~~La~~l~   28 (178)
T 1qhx_A           14 AGKSGIVRCLQSVLP   28 (178)
T ss_dssp             SSHHHHHHHHHHHSS
T ss_pred             CCHHHHHHHHHHhcC
Confidence            699999999999864

>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=84.18  E-value=2.3  Score=34.20  Aligned_cols=75  Identities=13%  Similarity=0.048  Sum_probs=41.4

Q ss_pred             CchhHHHHHHHHHhhCCCc----ceEEEeeccccccCCCChHHHHHHHHHHH--h------cCCCC--cC------chHH
Q 039644            1 IGKTAIARAIFDKISGDFE----CSCFLENVREESQRPGGLACLRQKLLSNI--L------KDKNV--MP------YIDL   60 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~----~~~wv~~~~~~~~~~~~~~~~~~~l~~~~--~------~~~~~--~~------~~~~   60 (192)
                      +|||+|+.++++....+.+    .++++- +++..   ....++...+...=  .      ...++  ..      ..-.
T Consensus       162 ~GKt~L~~~Ia~~~~~~~d~~~~~~V~~~-iGeR~---~Ev~e~~~~~~~~g~~~rtvvV~atsd~p~~~r~~a~~~a~t  237 (465)
T 3vr4_D          162 LPHKELAAQIARQATVLDSSDDFAVVFAA-IGITF---EEAEFFMEDFRQTGAIDRSVMFMNLANDPAIERIATPRMALT  237 (465)
T ss_dssp             SCHHHHHHHHHHHCBCSSCSSCEEEEEEE-EEECH---HHHHHHHHHHHHHTGGGGEEEEEEETTSCHHHHHHHHHHHHH
T ss_pred             cChHHHHHHHHHHHHhccCCCceEEEEEE-ecCCc---HHHHHHHHHHhhcCCccceEEEEECCCCCHHHHHHHHHHHHH
Confidence            6999999999987655333    344443 33311   34666666654421  0      11111  11      2223


Q ss_pred             HHhhc---CCceEEEEEeCCCC
Q 039644           61 NFRRL---SRMKVLIVFDDVTC   79 (192)
Q Consensus        61 l~~~l---~~~~~LlVlDdv~~   79 (192)
                      +.+++   .+++.|+++||+..
T Consensus       238 iAEyfrd~~G~~VLl~~DslTr  259 (465)
T 3vr4_D          238 AAEYLAYEKGMHVLVIMTDMTN  259 (465)
T ss_dssp             HHHHHHHTTCCEEEEEEECHHH
T ss_pred             HHHHHHHhcCCeEEEEEcChHH
Confidence            44444   36899999999953

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=83.61  E-value=0.15  Score=40.31  Aligned_cols=16  Identities=38%  Similarity=0.515  Sum_probs=13.6

Q ss_pred             CchhHHHHHHHHHhhC
Q 039644            1 IGKTAIARAIFDKISG   16 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~   16 (192)
                      +|||+|+.++++.+..
T Consensus       186 ~GKT~Ll~~Ia~~i~~  201 (427)
T 3l0o_A          186 AGKTTILKEIANGIAE  201 (427)
T ss_dssp             CCHHHHHHHHHHHHHH
T ss_pred             CChhHHHHHHHHHHhh
Confidence            6999999999997654

>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=82.74  E-value=2.5  Score=29.94  Aligned_cols=20  Identities=20%  Similarity=0.637  Sum_probs=16.4

Q ss_pred             CchhHHHHHHHHHhhCCCcc
Q 039644            1 IGKTAIARAIFDKISGDFEC   20 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~   20 (192)
                      +||||+++.+++.+...++.
T Consensus        13 sGKsTq~~~L~~~L~~~~~v   32 (205)
T 4hlc_A           13 SGKTTVINEVYHRLVKDYDV   32 (205)
T ss_dssp             SCHHHHHHHHHHHHTTTSCE
T ss_pred             CcHHHHHHHHHHHHHCCCCE
Confidence            69999999999988665544

>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=82.59  E-value=1.6  Score=34.87  Aligned_cols=17  Identities=41%  Similarity=0.538  Sum_probs=14.4

Q ss_pred             CchhHHHHHHHHHhhCC
Q 039644            1 IGKTAIARAIFDKISGD   17 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~   17 (192)
                      +|||+||+.+++.+...
T Consensus        74 tGKT~la~ala~~l~~~   90 (456)
T 2c9o_A           74 TGKTALALAIAQELGSK   90 (456)
T ss_dssp             SSHHHHHHHHHHHHCTT
T ss_pred             CCHHHHHHHHHHHhCCC
Confidence            69999999999987543

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=82.47  E-value=1.4  Score=35.87  Aligned_cols=13  Identities=31%  Similarity=0.685  Sum_probs=11.4

Q ss_pred             CCceEEEEEeCCC
Q 039644           66 SRMKVLIVFDDVT   78 (192)
Q Consensus        66 ~~~~~LlVlDdv~   78 (192)
                      .+++.|+++||+.
T Consensus       252 ~G~dVLl~~Dslt  264 (502)
T 2qe7_A          252 KGKHALVVYDDLS  264 (502)
T ss_dssp             TTCEEEEEEECHH
T ss_pred             cCCcEEEEEecHH
Confidence            4789999999994

>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=81.72  E-value=0.67  Score=31.20  Aligned_cols=15  Identities=13%  Similarity=0.182  Sum_probs=13.2

Q ss_pred             CchhHHHHHHHHHhh
Q 039644            1 IGKTAIARAIFDKIS   15 (192)
Q Consensus         1 iGKTtLa~~~~~~~~   15 (192)
                      +||||+|+.+..++.
T Consensus        12 sGKsT~~~~L~~~l~   26 (173)
T 3kb2_A           12 CFKSTVAAKLSKELK   26 (173)
T ss_dssp             SSHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHhC
Confidence            699999999998764

>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=81.20  E-value=0.45  Score=36.96  Aligned_cols=51  Identities=6%  Similarity=0.049  Sum_probs=35.8

Q ss_pred             chHHHHhhcCCceEEEEEeCCCCchhHHHhhccCCCCCCCceEEEEecchhHHh
Q 039644           57 YIDLNFRRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLR  110 (192)
Q Consensus        57 ~~~~l~~~l~~~~~LlVlDdv~~~~~~~~l~~~~~~~~~~~~iivTtR~~~~~~  110 (192)
                      ....+...|...+=+|++|...+.+.++.+....   ..|.-|++|+.......
T Consensus       185 ~~~~La~aL~~~PdvillDEp~d~e~~~~~~~~~---~~G~~vl~t~H~~~~~~  235 (356)
T 3jvv_A          185 FSEALRSALREDPDIILVGEMRDLETIRLALTAA---ETGHLVFGTLHTTSAAK  235 (356)
T ss_dssp             HHHHHHHHTTSCCSEEEESCCCSHHHHHHHHHHH---HTTCEEEEEESCSSHHH
T ss_pred             HHHHHHHHhhhCcCEEecCCCCCHHHHHHHHHHH---hcCCEEEEEEccChHHH
Confidence            4557888888899999999999766655544331   23555888887766553

>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=81.18  E-value=1.7  Score=35.42  Aligned_cols=14  Identities=29%  Similarity=0.603  Sum_probs=11.9

Q ss_pred             CCceEEEEEeCCCC
Q 039644           66 SRMKVLIVFDDVTC   79 (192)
Q Consensus        66 ~~~~~LlVlDdv~~   79 (192)
                      .+++.|+++||+..
T Consensus       260 ~G~dVLli~Dsltr  273 (510)
T 2ck3_A          260 NGKHALIIYDDLSK  273 (510)
T ss_dssp             TTCEEEEEEETHHH
T ss_pred             cCCcEEEEEcCHHH
Confidence            47899999999953

>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=81.14  E-value=1.3  Score=36.14  Aligned_cols=14  Identities=36%  Similarity=0.610  Sum_probs=11.8

Q ss_pred             CCceEEEEEeCCCC
Q 039644           66 SRMKVLIVFDDVTC   79 (192)
Q Consensus        66 ~~~~~LlVlDdv~~   79 (192)
                      .+++.|+++||+..
T Consensus       265 ~G~dVLli~DslTr  278 (515)
T 2r9v_A          265 SGRDALVVYDDLSK  278 (515)
T ss_dssp             TTCEEEEEEETHHH
T ss_pred             cCCcEEEEeccHHH
Confidence            47899999999953

>1fx0_A ATP synthase alpha chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_A*

Probab=80.88  E-value=3.3  Score=33.70  Aligned_cols=15  Identities=27%  Similarity=0.503  Sum_probs=12.4

Q ss_pred             CCceEEEEEeCCCCc
Q 039644           66 SRMKVLIVFDDVTCF   80 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~   80 (192)
                      .+++.|+++||+...
T Consensus       253 ~G~dVLli~Dsltr~  267 (507)
T 1fx0_A          253 RERHTLIIYDDLSKQ  267 (507)
T ss_dssp             TTCEEEEEEECHHHH
T ss_pred             cCCcEEEEEecHHHH
Confidence            589999999998543

>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=80.46  E-value=5.4  Score=32.49  Aligned_cols=14  Identities=29%  Similarity=0.560  Sum_probs=12.0

Q ss_pred             CCceEEEEEeCCCC
Q 039644           66 SRMKVLIVFDDVTC   79 (192)
Q Consensus        66 ~~~~~LlVlDdv~~   79 (192)
                      .+++.||++||+..
T Consensus       252 ~G~dVLli~Dsltr  265 (513)
T 3oaa_A          252 RGEDALIIYDDLSK  265 (513)
T ss_dssp             TTCEEEEEEETHHH
T ss_pred             cCCCEEEEecChHH
Confidence            57899999999953

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=80.27  E-value=1.5  Score=29.97  Aligned_cols=16  Identities=13%  Similarity=0.418  Sum_probs=14.0

Q ss_pred             CchhHHHHHHHHHhhC
Q 039644            1 IGKTAIARAIFDKISG   16 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~   16 (192)
                      +||||+|+.+++++..
T Consensus        12 sGKsT~~~~L~~~l~~   27 (194)
T 1nks_A           12 VGKSTVLAKVKEILDN   27 (194)
T ss_dssp             SCHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHh
Confidence            6999999999998764

>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=80.13  E-value=2.1  Score=32.37  Aligned_cols=14  Identities=29%  Similarity=0.290  Sum_probs=12.1

Q ss_pred             CchhHHHHHHHHHh
Q 039644            1 IGKTAIARAIFDKI   14 (192)
Q Consensus         1 iGKTtLa~~~~~~~   14 (192)
                      +|||+||.+++...
T Consensus       109 sGKT~la~~la~~~  122 (322)
T 2i1q_A          109 SGKTQIMHQSCVNL  122 (322)
T ss_dssp             SSHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHH
Confidence            69999999999853

---

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	192
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	1e-21

>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 = 87.2 bits (215), Expect = 1e-21
 Identities = 32/202 (15%), Positives = 64/202 (31%), Gaps = 21/202 (10%)

Query: 1   IGKTAIARAIFDK----ISGDFECSCFLENVREESQRP------GGLACLRQKLLSNILK 50
            GK+ IA     K    I  +++   +L++     +          L    +  L N   
Sbjct: 55  SGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPS 114

Query: 51  DKNVMPYIDLNF---RRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQ 107
            ++V   +         + R   L VFDDV                    R ++TTR+ +
Sbjct: 115 VEHVTSVVLKRMICNALIDRPNTLFVFDDV------VQEETIRWAQELRLRCLVTTRDVE 168

Query: 108 VLRN-WGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKV 166
           +        +  E+ +LE     +    +       +   E + +   + + G P  L +
Sbjct: 169 ISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGE-KEEDVLNKTIELSSGNPATLMM 227

Query: 167 LSCFLHKREKEVWESAIDKLQR 188
                  +  E      +KL+ 
Sbjct: 228 FFKSCEPKTFEKMAQLNNKLES 249

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	192
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	100.0
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.76
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.16
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	97.9
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	97.9
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	97.88
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.75
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	97.7
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	97.59
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	97.5
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	97.44
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	97.28
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	97.28
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	97.26
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	96.99
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	96.98
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	96.68
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	96.66
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	96.14
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	96.07
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	95.6
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	95.28
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	94.86
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	94.2
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	93.38
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	92.14
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	91.49
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	91.36
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	91.36
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	91.34
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	91.3
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	90.86
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	90.41
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	89.64
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	89.29
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	88.72
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	88.31
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	87.67
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	87.19
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	87.1
d1xpua3	289	Transcription termination factor Rho, ATPase domai	87.03
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	86.85
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	86.84
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	86.54
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	86.48
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	86.41
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	85.87
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	85.73
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	85.19
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	83.96
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	83.71
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	83.67
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	82.94
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	82.94
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	82.49
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	80.96

>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=2.9e-32  Score=205.96  Aligned_cols=177  Identities=17%  Similarity=0.158  Sum_probs=137.2

Q ss_pred             CchhHHHHHHHHH----hhCCCcceEEEeeccccccCCCChHHHHHHH---HHHHhcCCCC-----cC------chHHHH
Q 039644            1 IGKTAIARAIFDK----ISGDFECSCFLENVREESQRPGGLACLRQKL---LSNILKDKNV-----MP------YIDLNF   62 (192)
Q Consensus         1 iGKTtLa~~~~~~----~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l---~~~~~~~~~~-----~~------~~~~l~   62 (192)
                      |||||||+++|++    ...+|++++|+++.+.     ++...+...+   +.........     .+      ....+.
T Consensus        55 iGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~-----~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  129 (277)
T d2a5yb3          55 SGKSVIASQALSKSDQLIGINYDSIVWLKDSGT-----APKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICN  129 (277)
T ss_dssp             SSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCC-----STTHHHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhhhhhhhhcCceEEEEEecCC-----CCHHHHHHHHHHHHHHhcchhhcCCccchhhhhHHHHHHHHH
Confidence            7999999999985    5667999999985443     3444444444   3333322111     11      233466


Q ss_pred             hhcCCceEEEEEeCCCCchhHHHhhccCCCCCCCceEEEEecchhHHhhcCC-CceEecCCCCHHHHHHHHHHhhcCCCC
Q 039644           63 RRLSRMKVLIVFDDVTCFSQLESLMGSLDWLTPVSRIILTTRNKQVLRNWGV-SKIYEMEALEYHHALELFSQHAFKRNH  141 (192)
Q Consensus        63 ~~l~~~~~LlVlDdv~~~~~~~~l~~~~~~~~~~~~iivTtR~~~~~~~~~~-~~~~~l~~l~~~ea~~lf~~~~~~~~~  141 (192)
                      ..+.++++|+||||+|+..+|+.+.      ..+|+||||||++.++..+.. .+.+++++|+.+||++||...++....
T Consensus       130 ~~L~~kr~LlVLDDv~~~~~~~~~~------~~~srilvTTR~~~v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~  203 (277)
T d2a5yb3         130 ALIDRPNTLFVFDDVVQEETIRWAQ------ELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPV  203 (277)
T ss_dssp             HHTTSTTEEEEEEEECCHHHHHHHH------HTTCEEEEEESBGGGGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC-
T ss_pred             HHhccCCeeEecchhhHHhhhhhhc------ccCceEEEEeehHHHHHhcCCCCceEECCCCCHHHHHHHHHHHhCCccC
Confidence            7778999999999999999888764      247899999999999887643 468999999999999999998876544


Q ss_pred             CCccHHHHHHHHHHHhCCCchHHHHHHHHhccCCHHHHHHHHHHHHhc
Q 039644          142 PDVGYEKLSSNVTKYAQGIPLALKVLSCFLHKREKEVWESAIDKLQRI  189 (192)
Q Consensus       142 ~~~~~~~~~~~i~~~~~g~Plai~~~~~~l~~~~~~~w~~~l~~l~~~  189 (192)
                       .+...+.+++|+++|+|+|||++++|+.|+.++.+.|.+..+++++.
T Consensus       204 -~~~~~~~~~~iv~~c~GlPLAl~~ig~~l~~k~~~~~~~~~~~L~~~  250 (277)
T d2a5yb3         204 -GEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNKLESR  250 (277)
T ss_dssp             --CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSSSHHHHHHHHHHHHHH
T ss_pred             -chhhHHHHHHHHHHhCCCHHHHHHHHHHhccCCHHHHHHHHHHHhcC
Confidence             34567888999999999999999999999998899999998888753

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.76  E-value=1e-07  Score=69.48  Aligned_cols=165  Identities=16%  Similarity=0.149  Sum_probs=89.7

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcC-------------C--------------C
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKD-------------K--------------N   53 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~-------------~--------------~   53 (192)
                      +|||+|+++++++....+   .|+...............+...+.......             .              .
T Consensus        40 ~GKTsLl~~~~~~~~~~~---~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  116 (283)
T d2fnaa2          40 TGKSSIIKIGINELNLPY---IYLDLRKFEERNYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWN  116 (283)
T ss_dssp             SSHHHHHHHHHHHHTCCE---EEEEGGGGTTCSCCCHHHHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC--
T ss_pred             CcHHHHHHHHHHHCCCCe---EEEEeccccccccccHHHHHHHHHHHhhhhhhhhHHHHHHHHhhhcccccccccccccc
Confidence            799999999998876544   344322221222234455555544433210             0              0


Q ss_pred             C--cCchHHHHhh---cCCceEEEEEeCCCCchh------HHHhhccCCCCCCCceEEEEecchhHHhhc----------
Q 039644           54 V--MPYIDLNFRR---LSRMKVLIVFDDVTCFSQ------LESLMGSLDWLTPVSRIILTTRNKQVLRNW----------  112 (192)
Q Consensus        54 ~--~~~~~~l~~~---l~~~~~LlVlDdv~~~~~------~~~l~~~~~~~~~~~~iivTtR~~~~~~~~----------  112 (192)
                      .  ......+...   ...+++++++|++.....      +..+..... .......+++.+........          
T Consensus       117 ~~~~~~~~~~l~~l~~~~~~~~~i~id~~~~~~~~~~~~~~~~l~~~~~-~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~  195 (283)
T d2fnaa2         117 RKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPALAYAYD-NLKRIKFIMSGSEMGLLYDYLRVEDPESPL  195 (283)
T ss_dssp             ---CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGCTTCCCHHHHHHHHH-HCTTEEEEEEESSHHHHHHHTTTTCTTSTT
T ss_pred             hhhhhHHHHHHHHHHhhcccccccccchhhhhcccchHHHHHHHHHHHH-hhhhhhhhhccccchHHHHHHHhhhhcchh
Confidence            0  0012222222   356899999999864321      222221111 12333455554443322211          


Q ss_pred             --CCCceEecCCCCHHHHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCCchHHHHHHHHhcc
Q 039644          113 --GVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCFLHK  173 (192)
Q Consensus       113 --~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plai~~~~~~l~~  173 (192)
                        .....+.|++++.+++.+++...........+.    ..++.+.++|+|..+..++..+..
T Consensus       196 ~~~~~~~i~L~~l~~~e~~~~l~~~~~~~~~~~~~----~~~i~~~~~G~P~~L~~~~~~~~~  254 (283)
T d2fnaa2         196 FGRAFSTVELKPFSREEAIEFLRRGFQEADIDFKD----YEVVYEKIGGIPGWLTYFGFIYLD  254 (283)
T ss_dssp             TTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCCC----HHHHHHHHCSCHHHHHHHHHHHHH
T ss_pred             cccceeEEeeCCCCHHHHHHHHHhhhhhcCCCHHH----HHHHHHHhCCCHHHHHHHHHHHHh
Confidence              123568899999999999987755322221222    458999999999999999876543

>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=98.16  E-value=4.3e-05  Score=53.41  Aligned_cols=91  Identities=13%  Similarity=0.134  Sum_probs=64.2

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      +++-++|+|+++...  ....+...+.....++.+|++|++.. +.... +....+.+.+++.++....+.....     
T Consensus       107 ~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~~~ll~tI~SRc~~i~~~~~~~~~~~~~L~~~~~-----  181 (207)
T d1a5ta2         107 GGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREVT-----  181 (207)
T ss_dssp             SSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHCC-----
T ss_pred             CccceEEechhhhhhhhhhHHHHHHHHhhcccceeeeeecChhhhhhhhcceeEEEecCCCCHHHHHHHHHHcCC-----
Confidence            456699999999654  35666665665567788888887754 22222 5567899999999999988865431     


Q ss_pred             CccHHHHHHHHHHHhCCCchHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLAL  164 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Plai  164 (192)
                        ..++....+++.++|.|..+
T Consensus       182 --~~~~~~~~i~~~s~Gs~r~a  201 (207)
T d1a5ta2         182 --MSQDALLAALRLSAGSPGAA  201 (207)
T ss_dssp             --CCHHHHHHHHHHTTTCHHHH
T ss_pred             --CCHHHHHHHHHHcCCCHHHH
Confidence              12355677888899988654

>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=97.90  E-value=8e-05  Score=52.43  Aligned_cols=148  Identities=12%  Similarity=0.134  Sum_probs=84.4

Q ss_pred             CchhHHHHHHHHHhhCCC-cceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKISGDF-ECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F-~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~   79 (192)
                      +||||+|+.+++.+...+ ...++..+.++.    .+...+...+.........          ....+.-++|+|+++.
T Consensus        47 ~GKTt~a~~la~~l~~~~~~~~~~~~n~~~~----~~~~~i~~~~~~~~~~~~~----------~~~~~~kviiiDe~d~  112 (224)
T d1sxjb2          47 IGKTTSVHCLAHELLGRSYADGVLELNASDD----RGIDVVRNQIKHFAQKKLH----------LPPGKHKIVILDEADS  112 (224)
T ss_dssp             SSHHHHHHHHHHHHHGGGHHHHEEEECTTSC----CSHHHHHTHHHHHHHBCCC----------CCTTCCEEEEEESGGG
T ss_pred             CCchhhHHHHHHHHhcccccccccccccccc----CCceehhhHHHHHHHhhcc----------CCCcceEEEEEecccc
Confidence            699999999999765332 333333333331    3333333332222211111          0123456889999986


Q ss_pred             chh--HHHhhccCCCCCCCceEEEEecchhHH-hh-cCCCceEecCCCCHHHHHHHHHHhhcCCCCCCccHHHHHHHHHH
Q 039644           80 FSQ--LESLMGSLDWLTPVSRIILTTRNKQVL-RN-WGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTK  155 (192)
Q Consensus        80 ~~~--~~~l~~~~~~~~~~~~iivTtR~~~~~-~~-~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~  155 (192)
                      ...  ...+...+......+++++++...... .. .+....+.+++++.++....+...+.....  .-.++....|++
T Consensus       113 ~~~~~~~~ll~~~e~~~~~~~~i~~~~~~~~i~~~l~sr~~~i~~~~~~~~~i~~~l~~i~~~e~~--~i~~~~l~~I~~  190 (224)
T d1sxjb2         113 MTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDV--KYTNDGLEAIIF  190 (224)
T ss_dssp             SCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTC--CBCHHHHHHHHH
T ss_pred             cchhHHHHHhhhccccccceeeeeccCchhhhhhHHHHHHHHhhhcccchhhhHHHHHHHHHhccc--CCCHHHHHHHHH
Confidence            532  333333333344566777776654322 11 255678999999999998888776532111  123455778999


Q ss_pred             HhCCCchHH
Q 039644          156 YAQGIPLAL  164 (192)
Q Consensus       156 ~~~g~Plai  164 (192)
                      .|+|.+..+
T Consensus       191 ~s~Gd~R~a  199 (224)
T d1sxjb2         191 TAEGDMRQA  199 (224)
T ss_dssp             HHTTCHHHH
T ss_pred             HcCCcHHHH
Confidence            999987643

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.90  E-value=0.00016  Score=51.41  Aligned_cols=99  Identities=15%  Similarity=0.159  Sum_probs=64.8

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchhHHhh-c-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQVLRN-W-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~~~~~-~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      ++.-++|||+++...  ....+...+.....++++|++|.+...... . +....+.+.+++.++..+.+...+..... 
T Consensus       114 ~~~kviiIde~d~l~~~~q~~Llk~lE~~~~~~~~il~tn~~~~i~~~i~SRc~~i~~~~~~~~~i~~~l~~i~~~e~~-  192 (239)
T d1njfa_         114 GRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHI-  192 (239)
T ss_dssp             SSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTC-
T ss_pred             CCCEEEEEECcccCCHHHHHHHHHHHhcCCCCeEEEEEcCCccccChhHhhhhcccccccCcHHHhhhHHHHHHhhhcc-
Confidence            345689999998753  234455545445567788888876442221 1 55678999999999988877766532221 


Q ss_pred             CccHHHHHHHHHHHhCCCch-HHHHH
Q 039644          143 DVGYEKLSSNVTKYAQGIPL-ALKVL  167 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Pl-ai~~~  167 (192)
                       ...++....|++.++|.+. |+..+
T Consensus       193 -~~~~~~l~~i~~~s~Gd~R~ain~l  217 (239)
T d1njfa_         193 -AHEPRALQLLARAAEGSLRDALSLT  217 (239)
T ss_dssp             -CBCHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             -CCCHHHHHHHHHHcCCCHHHHHHHH
Confidence             2234556788999999886 44443

>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=97.88  E-value=0.00016  Score=50.78  Aligned_cols=145  Identities=12%  Similarity=0.167  Sum_probs=82.5

Q ss_pred             CchhHHHHHHHHHhhCC-CcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCC
Q 039644            1 IGKTAIARAIFDKISGD-FECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTC   79 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~-F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~   79 (192)
                      +||||+|+.+++.+... |...+.....+..    ..... .............          ...++.-++|+|+++.
T Consensus        46 ~GKttl~~~la~~l~~~~~~~~~~e~~~~~~----~~~~~-~~~~~~~~~~~~~----------~~~~~~kiiiiDe~d~  110 (227)
T d1sxjc2          46 TGKTSTIVALAREIYGKNYSNMVLELNASDD----RGIDV-VRNQIKDFASTRQ----------IFSKGFKLIILDEADA  110 (227)
T ss_dssp             SSHHHHHHHHHHHHHTTSHHHHEEEECTTSC----CSHHH-HHTHHHHHHHBCC----------SSSCSCEEEEETTGGG
T ss_pred             CChhHHHHHHHHHhhcCCCcceeEEeccccc----CCeee-eecchhhcccccc----------ccCCCeEEEEEecccc
Confidence            69999999999976433 2222222222211    22222 2222222211111          1123445889999986


Q ss_pred             ch--hHHHhhccCCCCCCCceEEEEecchhHHhh--cCCCceEecCCCCHHHHHHHHHHhhcCCCCCCccHHHHHHHHHH
Q 039644           80 FS--QLESLMGSLDWLTPVSRIILTTRNKQVLRN--WGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTK  155 (192)
Q Consensus        80 ~~--~~~~l~~~~~~~~~~~~iivTtR~~~~~~~--~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~  155 (192)
                      ..  ....+...+......+.++++|........  ......+.+.+++.++....+.+.+.....  .-.++....|++
T Consensus       111 ~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~i~~~i~sr~~~i~~~~~~~~~i~~~l~~I~~~e~i--~i~~~~l~~i~~  188 (227)
T d1sxjc2         111 MTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKL--KLSPNAEKALIE  188 (227)
T ss_dssp             SCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHTTTC--CBCHHHHHHHHH
T ss_pred             chhhHHHHHHHHhhhcccceeeccccCcHHHhHHHHHHHHhhhccccccccccccccccccccccc--cCCHHHHHHHHH
Confidence            53  234444444444567778888766432221  255678999999999999888876643221  123455678999


Q ss_pred             HhCCCch
Q 039644          156 YAQGIPL  162 (192)
Q Consensus       156 ~~~g~Pl  162 (192)
                      .++|...
T Consensus       189 ~s~Gd~R  195 (227)
T d1sxjc2         189 LSNGDMR  195 (227)
T ss_dssp             HHTTCHH
T ss_pred             HcCCcHH
Confidence            9998764

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=97.75  E-value=8.2e-05  Score=52.21  Aligned_cols=118  Identities=14%  Similarity=0.178  Sum_probs=64.7

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCCCCc
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDVTCF   80 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv~~~   80 (192)
                      +|||.|+..++++.......++++.           ..++...+...+...     ....+...++ .--+|+|||++..
T Consensus        47 ~GKTHLl~A~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~-----~~~~~~~~~~-~~dll~iDDi~~i  109 (213)
T d1l8qa2          47 TGKTHLLQAAGNEAKKRGYRVIYSS-----------ADDFAQAMVEHLKKG-----TINEFRNMYK-SVDLLLLDDVQFL  109 (213)
T ss_dssp             SSHHHHHHHHHHHHHHTTCCEEEEE-----------HHHHHHHHHHHHHHT-----CHHHHHHHHH-TCSEEEEECGGGG
T ss_pred             CcHHHHHHHHHHHhccCccceEEec-----------hHHHHHHHHHHHHcc-----chhhHHHHHh-hccchhhhhhhhh
Confidence            6999999999998766666666664           334444444444332     1122222222 2348999999743


Q ss_pred             ---hhHHH-hhccCCC-CCCCceEEEEecchh---------HHhhcCCCceEecCCCCHHHHHHHHHHhh
Q 039644           81 ---SQLES-LMGSLDW-LTPVSRIILTTRNKQ---------VLRNWGVSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus        81 ---~~~~~-l~~~~~~-~~~~~~iivTtR~~~---------~~~~~~~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                         ..|+. +...+.. ...|.++|+||+...         ..........+.++ .+.++-.+++++.+
T Consensus       110 ~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~~~dL~SRL~~g~~~~i~-p~d~~~~~iL~~~a  178 (213)
T d1l8qa2         110 SGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIE-LDNKTRFKIIKEKL  178 (213)
T ss_dssp             TTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECC-CCHHHHHHHHHHHH
T ss_pred             cCchHHHHHHHHHHHHHhhccceEEEecCCcchhccccchHHHHHhhCceEEEEC-CCcHHHHHHHHHHH
Confidence               23432 2222211 236778999998643         22222334556664 35555555655554

>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=97.70  E-value=0.00031  Score=49.48  Aligned_cols=154  Identities=14%  Similarity=0.137  Sum_probs=81.3

Q ss_pred             CchhHHHHHHHHHhhCCC---cceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCC
Q 039644            1 IGKTAIARAIFDKISGDF---ECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDV   77 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F---~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv   77 (192)
                      +||||+|+.+++++....   .....+. .+..    ....... ...+..............+........-++|+|++
T Consensus        44 ~GKTtl~~~i~~~l~~~~~~~~~~~~~~-~~~~----~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~viiiDe~  117 (237)
T d1sxjd2          44 TGKTSTILALTKELYGPDLMKSRILELN-ASDE----RGISIVR-EKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEA  117 (237)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHTTSEEEEC-SSSC----CCHHHHT-THHHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTG
T ss_pred             CChHHHHHHHHHHHcCCcccccchhhee-cccc----ccchHHH-HHHHHHhhhhhhhhhHHHHhhccccCceEEEEecc
Confidence            699999999999753221   1122222 2221    2333222 22222222211111222233333444447999999


Q ss_pred             CCch--hHHHhhccCCCCCCCceEEEEecchh-HHh-hcCCCceEecCCCCHHHHHHHHHHhhcCCCCCCccHHHHHHHH
Q 039644           78 TCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLR-NWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNV  153 (192)
Q Consensus        78 ~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~-~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i  153 (192)
                      +...  ....+...+......+++++++.... ... .......+.+++++.++..+++.+.+....-  .-.++....|
T Consensus       118 d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~l~sr~~~i~f~~~~~~~~~~~L~~i~~~e~i--~i~~~~l~~i  195 (237)
T d1sxjd2         118 DSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFISEQENV--KCDDGVLERI  195 (237)
T ss_dssp             GGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEEECCCCCHHHHHHHHHHHHHTTTC--CCCHHHHHHH
T ss_pred             cccCHHHHHHHhhccccccccccccccccccccccccccchhhhhccccccccccchhhhhhhhhhcC--cCCHHHHHHH
Confidence            8553  23333322223345566777665432 111 1133467999999999999998876643221  2234567788


Q ss_pred             HHHhCCCch
Q 039644          154 TKYAQGIPL  162 (192)
Q Consensus       154 ~~~~~g~Pl  162 (192)
                      ++.++|-+.
T Consensus       196 a~~s~gd~R  204 (237)
T d1sxjd2         196 LDISAGDLR  204 (237)
T ss_dssp             HHHTSSCHH
T ss_pred             HHHcCCCHH
Confidence            899988653

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=97.59  E-value=0.00032  Score=49.36  Aligned_cols=95  Identities=13%  Similarity=0.121  Sum_probs=59.2

Q ss_pred             CceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchh-HHhhc-CCCceEecCCCCHHHHHHHHHHhhcCCCCC
Q 039644           67 RMKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQ-VLRNW-GVSKIYEMEALEYHHALELFSQHAFKRNHP  142 (192)
Q Consensus        67 ~~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~  142 (192)
                      .+..++++|+++...  .+..+...+........+|.+|.... +.... +....+.+.+.+.++....+.+.+....  
T Consensus       108 ~~~~iilide~d~~~~~~~~~ll~~l~~~~~~~~~i~~~n~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~~~~~e~--  185 (231)
T d1iqpa2         108 ASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEG--  185 (231)
T ss_dssp             CSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEECCCCCHHHHHHHHHHHHHTTT--
T ss_pred             CCceEEeehhhhhcchhHHHHHhhhcccCCcceEEEeccCChhhchHhHhCccccccccccchhhHHHHHHHHHHHhC--
Confidence            456789999997542  34444443333344456666665433 21111 3456799999999999988887764322  


Q ss_pred             CccHHHHHHHHHHHhCCCchH
Q 039644          143 DVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       143 ~~~~~~~~~~i~~~~~g~Pla  163 (192)
                      -.-.++..+.|++.++|....
T Consensus       186 i~i~~~~l~~I~~~~~gdiR~  206 (231)
T d1iqpa2         186 LELTEEGLQAILYIAEGDMRR  206 (231)
T ss_dssp             CEECHHHHHHHHHHHTTCHHH
T ss_pred             CCCCHHHHHHHHHHcCCCHHH
Confidence            122345677899999987553

>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=97.50  E-value=0.00043  Score=49.12  Aligned_cols=95  Identities=6%  Similarity=0.081  Sum_probs=56.9

Q ss_pred             ceEEEEEeCCCCch--hHHHhhccCCCCCCCceEEEEecchhHH-hh-cCCCceEecCCCCHHHHHHHHHHhhcCCCCCC
Q 039644           68 MKVLIVFDDVTCFS--QLESLMGSLDWLTPVSRIILTTRNKQVL-RN-WGVSKIYEMEALEYHHALELFSQHAFKRNHPD  143 (192)
Q Consensus        68 ~~~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~~~-~~-~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~  143 (192)
                      +.-++|||+++...  .+..+...+......+++|+||...... .. .+....+++.+++.++..+++...+-.... .
T Consensus       131 ~~~iiiide~d~l~~~~~~~l~~~~e~~~~~~~~Il~tn~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~i~~~e~~-~  209 (252)
T d1sxje2         131 RYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERI-Q  209 (252)
T ss_dssp             CCEEEEEECTTSSCHHHHHHHHHHHHHSTTTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTC-E
T ss_pred             CceEEEeccccccccccchhhhcccccccccccceeeeccccchhhhhhcchheeeecccchhhHHHHHHHHHHHcCC-C
Confidence            44589999998753  2344433333344567777777654311 11 123467899999999999888765422111 1


Q ss_pred             ccHHHHHHHHHHHhCCCchH
Q 039644          144 VGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       144 ~~~~~~~~~i~~~~~g~Pla  163 (192)
                      ...++..+.|++.+.|.+..
T Consensus       210 ~~~~~~l~~i~~~s~Gd~R~  229 (252)
T d1sxje2         210 LETKDILKRIAQASNGNLRV  229 (252)
T ss_dssp             ECCSHHHHHHHHHHTTCHHH
T ss_pred             CCcHHHHHHHHHHcCCcHHH
Confidence            11234566788999888754

>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=97.44  E-value=0.008  Score=42.42  Aligned_cols=131  Identities=13%  Similarity=0.179  Sum_probs=73.0

Q ss_pred             CchhHHHHHHHHHhhCCCcc-eEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-cC----chHHHHhhc--CCceEEE
Q 039644            1 IGKTAIARAIFDKISGDFEC-SCFLENVREESQRPGGLACLRQKLLSNILKDKNV-MP----YIDLNFRRL--SRMKVLI   72 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~-~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~----~~~~l~~~l--~~~~~Ll   72 (192)
                      +|||++|+.+++.+...... .+++.....     .....+...+.......... ..    ....+...+  .......
T Consensus        54 tGKT~l~~~l~~~l~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (276)
T d1fnna2          54 TGKTVTLRKLWELYKDKTTARFVYINGFIY-----RNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFL  128 (276)
T ss_dssp             SSHHHHHHHHHHHHTTSCCCEEEEEETTTC-----CSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEE
T ss_pred             CCHHHHHHHHHHHHhcccCCcEEEecchhh-----hhhhhhhhhhHHhhhhhhhhhccchhHHHHHHHHHHhhccccccc
Confidence            69999999999988765543 334432222     56677777777766544333 21    333333333  3356777


Q ss_pred             EEeCCCCchh-----HHHhhccCCCC-CCCceEEEEecchhHHhhc-------CCCceEecCCCCHHHHHHHHHHhh
Q 039644           73 VFDDVTCFSQ-----LESLMGSLDWL-TPVSRIILTTRNKQVLRNW-------GVSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus        73 VlDdv~~~~~-----~~~l~~~~~~~-~~~~~iivTtR~~~~~~~~-------~~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      ++|.++....     ...+....... .....+|.++.........       .....+.+.+.+.++..+++..++
T Consensus       129 ~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~r~~~~~i~~~~~~~~e~~~il~~r~  205 (276)
T d1fnna2         129 VLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRA  205 (276)
T ss_dssp             EEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHH
T ss_pred             chhHHHHhhhhhhhhHHHHHhccccccccceEEeecCCchhhhhhcchhhhhhhcchhccccchhHHHHHHHHHHHH
Confidence            7888775432     12222111111 2233444555543322211       112457899999999999988754

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=97.28  E-value=0.0036  Score=44.44  Aligned_cols=17  Identities=35%  Similarity=0.313  Sum_probs=14.5

Q ss_pred             CchhHHHHHHHHHhhCC
Q 039644            1 IGKTAIARAIFDKISGD   17 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~   17 (192)
                      +|||++|+.+++.....
T Consensus        51 tGKT~la~alA~~~~~~   67 (246)
T d1d2na_          51 SGKTALAAKIAEESNFP   67 (246)
T ss_dssp             SSHHHHHHHHHHHHTCS
T ss_pred             CCHHHHHHHHhhccccc
Confidence            69999999999987544

>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=97.28  E-value=0.00048  Score=49.29  Aligned_cols=94  Identities=15%  Similarity=0.241  Sum_probs=52.2

Q ss_pred             CCceEEEEEeCCCCch----------------hHHHhhccCCCCC--CCceEEEEecchhHHhh-c----CCCceEecCC
Q 039644           66 SRMKVLIVFDDVTCFS----------------QLESLMGSLDWLT--PVSRIILTTRNKQVLRN-W----GVSKIYEMEA  122 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~~----------------~~~~l~~~~~~~~--~~~~iivTtR~~~~~~~-~----~~~~~~~l~~  122 (192)
                      ...+++|+|||++...                ....|...+....  .+.-||-||........ .    .-.+.+.+++
T Consensus        99 ~~~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~  178 (247)
T d1ixza_          99 RHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDA  178 (247)
T ss_dssp             TSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCS
T ss_pred             HcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCccccCHhHcCCCCCcEEEEECC
Confidence            4578999999985210                1223332222222  22223336665432222 1    2356889999


Q ss_pred             CCHHHHHHHHHHhhcCCC-CCCccHHHHHHHHHHHhCCCchH
Q 039644          123 LEYHHALELFSQHAFKRN-HPDVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       123 l~~~ea~~lf~~~~~~~~-~~~~~~~~~~~~i~~~~~g~Pla  163 (192)
                      .+.++-.++|........ ..+..+    ..+.+.+.|+.-+
T Consensus       179 P~~~eR~~il~~~l~~~~~~~~~~~----~~la~~t~g~s~~  216 (247)
T d1ixza_         179 PDVKGREQILRIHARGKPLAEDVDL----ALLAKRTPGFVGA  216 (247)
T ss_dssp             CCHHHHHHHHHHHHTTSCBCTTCCH----HHHHHTCTTCCHH
T ss_pred             cCHHHHHHHHHHHhcccCCccccCH----HHHHHHCCCCCHH
Confidence            999999999987764333 222233    4567778776443

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.26  E-value=0.0018  Score=45.81  Aligned_cols=152  Identities=14%  Similarity=0.138  Sum_probs=76.3

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcC--chHHHHhhcCCceEEEEEeCCC
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMP--YIDLNFRRLSRMKVLIVFDDVT   78 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~--~~~~l~~~l~~~~~LlVlDdv~   78 (192)
                      +||||+|+.+++++...   .+++. .++.    .....+ ...............  ...........+..++++|+++
T Consensus        63 ~GKTt~a~~la~~~~~~---~~~~~-~~~~----~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vi~ide~~  133 (253)
T d1sxja2          63 IGKTTAAHLVAQELGYD---ILEQN-ASDV----RSKTLL-NAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVD  133 (253)
T ss_dssp             SSHHHHHHHHHHHTTCE---EEEEC-TTSC----CCHHHH-HHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGG
T ss_pred             CCHHHHHHHHHHHHHhh---hhccc-cccc----hhhHHH-HHHHHHHhhcchhhhhhhhhhhcccccccceEEEeeecc
Confidence            69999999999976432   23443 3221    122222 222222222221111  1111222234567789999987


Q ss_pred             Cch-----hHHHhhccCCCCCCCceEEEEecch---hHHhhcCCCceEecCCCCHHHHHHHHHHhhcCCC-CCCccHHHH
Q 039644           79 CFS-----QLESLMGSLDWLTPVSRIILTTRNK---QVLRNWGVSKIYEMEALEYHHALELFSQHAFKRN-HPDVGYEKL  149 (192)
Q Consensus        79 ~~~-----~~~~l~~~~~~~~~~~~iivTtR~~---~~~~~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~-~~~~~~~~~  149 (192)
                      ...     .+..+.....  .....+++|+...   .+.........+.+.+.+.++-...+....-... .-++   +.
T Consensus       134 ~~~~~~~~~~~~~~~~~~--~~~~~ii~i~~~~~~~~~~~l~~~~~~i~f~~~~~~~i~~~l~~i~~~e~i~i~~---~~  208 (253)
T d1sxja2         134 GMSGGDRGGVGQLAQFCR--KTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDP---NV  208 (253)
T ss_dssp             GCCTTSTTHHHHHHHHHH--HCSSCEEEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCT---TH
T ss_pred             ccccchhhhhHHHhhhhc--ccccccccccccccccccccccceeeeeeccccchhHHHHHHHHHHHHhCCCCCH---HH
Confidence            432     1333322111  1122355554322   1222224457899999999998888777553211 1111   34


Q ss_pred             HHHHHHHhCCCc-hHHHH
Q 039644          150 SSNVTKYAQGIP-LALKV  166 (192)
Q Consensus       150 ~~~i~~~~~g~P-lai~~  166 (192)
                      ...|++.++|-. .||..
T Consensus       209 l~~i~~~s~GDiR~ai~~  226 (253)
T d1sxja2         209 IDRLIQTTRGDIRQVINL  226 (253)
T ss_dssp             HHHHHHHTTTCHHHHHHH
T ss_pred             HHHHHHhCCCcHHHHHHH
Confidence            567888999976 44433

>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=96.99  E-value=0.002  Score=46.16  Aligned_cols=94  Identities=14%  Similarity=0.166  Sum_probs=55.2

Q ss_pred             CCceEEEEEeCCCCch---------h----HHHhhccCC--CCCCCceEEEEecchhHHhhc-----CCCceEecCCCCH
Q 039644           66 SRMKVLIVFDDVTCFS---------Q----LESLMGSLD--WLTPVSRIILTTRNKQVLRNW-----GVSKIYEMEALEY  125 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~~---------~----~~~l~~~~~--~~~~~~~iivTtR~~~~~~~~-----~~~~~~~l~~l~~  125 (192)
                      ...+++|+|||++...         .    ...+...+.  ....+.-||.||.........     ...+.+.++..+.
T Consensus        95 ~~~p~il~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~vlvi~tTn~~~~ld~al~r~gRfd~~i~~~~P~~  174 (258)
T d1e32a2          95 KNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDA  174 (258)
T ss_dssp             HTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCCCSSCEEEEEEESCGGGSCGGGTSTTSSCEEEECCCCCH
T ss_pred             hcCCeEEEehhhhhhccCCCCCCCchHHHHHHHhccccccccccCCccEEEeCCCccccchhhhhcccccceeECCCCCH
Confidence            4678999999997431         0    112221111  122333455588765433222     2457899999999


Q ss_pred             HHHHHHHHHhhcCCCC-CCccHHHHHHHHHHHhCCCchH
Q 039644          126 HHALELFSQHAFKRNH-PDVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       126 ~ea~~lf~~~~~~~~~-~~~~~~~~~~~i~~~~~g~Pla  163 (192)
                      ++-.++|......... .+..    ...|++.+.|+--|
T Consensus       175 ~~R~~il~~~l~~~~~~~~~~----~~~la~~t~G~s~a  209 (258)
T d1e32a2         175 TGRLEILQIHTKNMKLADDVD----LEQVANETHGHVGA  209 (258)
T ss_dssp             HHHHHHHHHTTTTSCBCTTCC----HHHHHHHCTTCCHH
T ss_pred             HHHHHHhhhhccCcccccccc----hhhhhhcccCCCHH
Confidence            9999999876533221 1222    35788888887544

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=96.98  E-value=0.02  Score=40.45  Aligned_cols=131  Identities=11%  Similarity=0.169  Sum_probs=69.7

Q ss_pred             CchhHHHHHHHHHhhCCC------cceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC-cC----chHHHHhhc--CC
Q 039644            1 IGKTAIARAIFDKISGDF------ECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV-MP----YIDLNFRRL--SR   67 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F------~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~----~~~~l~~~l--~~   67 (192)
                      +|||++++.+++.+.+.+      ....++.....     .................... ..    ....+....  ..
T Consensus        57 tGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  131 (287)
T d1w5sa2          57 IGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNA-----PNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVEN  131 (287)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGC-----CSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHhhcccccCCceeeeeccccc-----cchhhHHHHHhhhcccccccccchHHHHHHHHHHHHHhcc
Confidence            699999999999754322      12333332221     45666666666666544433 11    334444444  34


Q ss_pred             ceEEEEEeCCCCch--------h---HHHhhccCCC---CCCCceEEEEecchhHHh--------hcCCCceEecCCCCH
Q 039644           68 MKVLIVFDDVTCFS--------Q---LESLMGSLDW---LTPVSRIILTTRNKQVLR--------NWGVSKIYEMEALEY  125 (192)
Q Consensus        68 ~~~LlVlDdv~~~~--------~---~~~l~~~~~~---~~~~~~iivTtR~~~~~~--------~~~~~~~~~l~~l~~  125 (192)
                      ...++++|.++...        .   +..+...+..   ......|++++.......        .......+.+++.+.
T Consensus       132 ~~~~~iide~d~l~~~~~~~~~~~~~l~~l~~~l~~~~~~~~~~~i~i~~~~~~~~~~~~~~~~~~~r~~~~i~f~~y~~  211 (287)
T d1w5sa2         132 HYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKS  211 (287)
T ss_dssp             CEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCH
T ss_pred             CccccceeEEEEeccccccchhHHHHHHHHHHhcchhhcccceeEEeecccHHHHHHHHhhccchhcccceeeeccCCcH
Confidence            57788888885321        1   1112221221   112223334443322111        112346788999999


Q ss_pred             HHHHHHHHHhh
Q 039644          126 HHALELFSQHA  136 (192)
Q Consensus       126 ~ea~~lf~~~~  136 (192)
                      ++..+++..++
T Consensus       212 ~el~~Il~~r~  222 (287)
T d1w5sa2         212 RELYTILEQRA  222 (287)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHhhhH
Confidence            99999998765

>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=96.68  E-value=0.0052  Score=44.09  Aligned_cols=94  Identities=13%  Similarity=0.211  Sum_probs=52.8

Q ss_pred             CCceEEEEEeCCCCch----------------hHHHhhccCCCCC--CCceEEEEecchhHHhh-c----CCCceEecCC
Q 039644           66 SRMKVLIVFDDVTCFS----------------QLESLMGSLDWLT--PVSRIILTTRNKQVLRN-W----GVSKIYEMEA  122 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~~----------------~~~~l~~~~~~~~--~~~~iivTtR~~~~~~~-~----~~~~~~~l~~  122 (192)
                      ...+++|+|||++...                ....+...+....  .+--||.||........ .    .....++++.
T Consensus        98 ~~~p~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gRf~~~i~~~~  177 (265)
T d1r7ra3          98 QAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPL  177 (265)
T ss_dssp             HTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC------CCEEEECCBSCTTTSCGGGSSTTSEEEEECCC
T ss_pred             hcCCcceeHHhhhhccccCCCcCCCCcHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCCchhCCHHHhCCCCccEEEEecc
Confidence            3568999999996321                1233444443322  23445557765543211 1    2356899999


Q ss_pred             CCHHHHHHHHHHhhcCCCC-CCccHHHHHHHHHHHhCCCchH
Q 039644          123 LEYHHALELFSQHAFKRNH-PDVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       123 l~~~ea~~lf~~~~~~~~~-~~~~~~~~~~~i~~~~~g~Pla  163 (192)
                      .+.++-.++|......... .+..    ..++.+.+.|+..|
T Consensus       178 p~~~~R~~il~~~l~~~~~~~~~~----l~~la~~t~g~s~~  215 (265)
T d1r7ra3         178 PDEKSRVAILKANLRKSPVAKDVD----LEFLAKMTNGFSGA  215 (265)
T ss_dssp             CCCHHHHHHHHHHTTCC----CCC----CHHHHHHHCSSCCH
T ss_pred             hHHHHHHHHHHHHhccCCchhhhh----HHHHHhcCCCCCHH
Confidence            9999999999876532111 1222    24677778877654

>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=96.66  E-value=0.0026  Score=45.54  Aligned_cols=94  Identities=14%  Similarity=0.197  Sum_probs=53.3

Q ss_pred             CCceEEEEEeCCCCc------------hh----HHHhhccCCC--CCCCceEEEEecchhHHhh-c----CCCceEecCC
Q 039644           66 SRMKVLIVFDDVTCF------------SQ----LESLMGSLDW--LTPVSRIILTTRNKQVLRN-W----GVSKIYEMEA  122 (192)
Q Consensus        66 ~~~~~LlVlDdv~~~------------~~----~~~l~~~~~~--~~~~~~iivTtR~~~~~~~-~----~~~~~~~l~~  122 (192)
                      ...|++|+|||++..            ..    +..+...+..  ...+.-||-||........ .    .-.+.+.++.
T Consensus       102 ~~~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~v~vIatTn~~~~ld~al~R~gRfd~~i~i~~  181 (256)
T d1lv7a_         102 KAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGL  181 (256)
T ss_dssp             TTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCC
T ss_pred             HcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCcccCCHhHcCCCCCCEEEECCC
Confidence            467899999999521            01    2233332222  2233344447776443221 1    2357899999


Q ss_pred             CCHHHHHHHHHHhhcCCCC-CCccHHHHHHHHHHHhCCCchH
Q 039644          123 LEYHHALELFSQHAFKRNH-PDVGYEKLSSNVTKYAQGIPLA  163 (192)
Q Consensus       123 l~~~ea~~lf~~~~~~~~~-~~~~~~~~~~~i~~~~~g~Pla  163 (192)
                      .+.++-.++|......... .+..    ...+.+.+.|+.-|
T Consensus       182 P~~~~R~~il~~~l~~~~~~~~~~----~~~la~~t~G~s~a  219 (256)
T d1lv7a_         182 PDVRGREQILKVHMRRVPLAPDID----AAIIARGTPGFSGA  219 (256)
T ss_dssp             CCHHHHHHHHHHHHTTSCBCTTCC----HHHHHHTCTTCCHH
T ss_pred             cCHHHHHHHHHHhccCCCcCcccC----HHHHHHhCCCCCHH
Confidence            9999989998877633221 2222    34567778887544

>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=96.14  E-value=0.095  Score=37.34  Aligned_cols=117  Identities=14%  Similarity=0.209  Sum_probs=67.8

Q ss_pred             CchhHHHHHHHHHhhC-----C-CcceEEEeeccccccC---CCChHHHHHHHHHHHhcCCCCcCchHHHHhhc-CCceE
Q 039644            1 IGKTAIARAIFDKISG-----D-FECSCFLENVREESQR---PGGLACLRQKLLSNILKDKNVMPYIDLNFRRL-SRMKV   70 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~-----~-F~~~~wv~~~~~~~~~---~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l-~~~~~   70 (192)
                      +|||+++..+++++..     . ....+|...++.....   .-...+                 ....+...+ ...+.
T Consensus        50 vGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~liag~~~~g~~e~-----------------r~~~i~~~~~~~~~i  112 (268)
T d1r6bx2          50 VGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEK-----------------RFKALLKQLEQDTNS  112 (268)
T ss_dssp             SSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---CCCCCSSCHHH-----------------HHHHHHHHHSSSSCE
T ss_pred             CcHHHHHHHHHHHHHhCCcccccccceeEEeeechHhccCccchhHHH-----------------HHHHHHHHhhccCCc
Confidence            6999999999997422     1 2345665322221100   012222                 222233333 34678


Q ss_pred             EEEEeCCCCch----------hHHHh-hccCCCCCCCceEEEEecchhHHhhcC-------CCceEecCCCCHHHHHHHH
Q 039644           71 LIVFDDVTCFS----------QLESL-MGSLDWLTPVSRIILTTRNKQVLRNWG-------VSKIYEMEALEYHHALELF  132 (192)
Q Consensus        71 LlVlDdv~~~~----------~~~~l-~~~~~~~~~~~~iivTtR~~~~~~~~~-------~~~~~~l~~l~~~ea~~lf  132 (192)
                      ++++|++...-          +...+ .+++.  .+.-++|.+|..+.......       .-+.+.+.+.+.+++..++
T Consensus       113 IlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~--rg~i~vIgatT~eey~~~~e~d~al~rrF~~I~V~Eps~e~t~~IL  190 (268)
T d1r6bx2         113 ILFIDEIHTIIGAGAASGGQVDAANLIKPLLS--SGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQII  190 (268)
T ss_dssp             EEEETTTTTTTTSCCSSSCHHHHHHHHSSCSS--SCCCEEEEEECHHHHHCCCCCTTSSGGGEEEEECCCCCHHHHHHHH
T ss_pred             eEEecchHHHhcCCCCCCccccHHHHhhHHHh--CCCCeEEEeCCHHHHHHHHhhcHHHHhhhcccccCCCCHHHHHHHH
Confidence            99999986431          23333 33332  34567888887766655442       2367889999999999998


Q ss_pred             HHhh
Q 039644          133 SQHA  136 (192)
Q Consensus       133 ~~~~  136 (192)
                      ....
T Consensus       191 ~~~~  194 (268)
T d1r6bx2         191 NGLK  194 (268)
T ss_dssp             HHHH
T ss_pred             HHhh
Confidence            7644

>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=96.07  E-value=0.12  Score=35.69  Aligned_cols=73  Identities=14%  Similarity=-0.023  Sum_probs=47.0

Q ss_pred             CCCceEecCCCCHHHHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCCchHHHHHHHH----hc--cCC---HHHHHHHH
Q 039644          113 GVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSCF----LH--KRE---KEVWESAI  183 (192)
Q Consensus       113 ~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plai~~~~~~----l~--~~~---~~~w~~~l  183 (192)
                      .....+.+...+.++...++.+.+....  -....+....|++.+.|.+-.+..+...    ..  +..   .+.+.+++
T Consensus       155 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~--i~~~~~~l~~ia~~s~gd~R~a~~~l~~~~~~a~~~~~~~It~~~~~~~l  232 (239)
T d1ixsb2         155 RFGIVEHLEYYTPEELAQGVMRDARLLG--VRITEEAALEIGRRSRGTMRVAKRLFRRVRDFAQVAGEEVITRERALEAL  232 (239)
T ss_dssp             GCSEEEECCCCCHHHHHHHHHHHHGGGC--CCBCHHHHHHHHHHTTSSHHHHHHHHHHHHHHHTTSCCSCBCHHHHHHHH
T ss_pred             ccceeeEeeccChhhhhHHHHHHHHHhC--CccchHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhCCCCcCHHHHHHHH
Confidence            4567788999999998888776653222  2233557788999999987665433322    11  222   67777777


Q ss_pred             HHHH
Q 039644          184 DKLQ  187 (192)
Q Consensus       184 ~~l~  187 (192)
                      ..+.
T Consensus       233 ~~l~  236 (239)
T d1ixsb2         233 AALG  236 (239)
T ss_dssp             HHHT
T ss_pred             hhhC
Confidence            6653

>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=95.60  E-value=0.19  Score=34.48  Aligned_cols=89  Identities=12%  Similarity=0.106  Sum_probs=53.0

Q ss_pred             CceEEEEecchhHHh---hcCCCceEecCCCCHHHHHHHHHHhhcCCCCCCccHHHHHHHHHHHhCCCchHHHHHHH---
Q 039644           96 VSRIILTTRNKQVLR---NWGVSKIYEMEALEYHHALELFSQHAFKRNHPDVGYEKLSSNVTKYAQGIPLALKVLSC---  169 (192)
Q Consensus        96 ~~~iivTtR~~~~~~---~~~~~~~~~l~~l~~~ea~~lf~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plai~~~~~---  169 (192)
                      ...+|.+|.......   .......+.++..+..+...++........  .....+....+++.++|.+-.+..+..   
T Consensus       134 ~~~~I~at~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~~~~l~~i~~~s~gd~R~ai~~l~~~~  211 (238)
T d1in4a2         134 PFTLVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMD--VEIEDAAAEMIAKRSRGTPRIAIRLTKRVR  211 (238)
T ss_dssp             CCEEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTT--CCBCHHHHHHHHHTSTTCHHHHHHHHHHHH
T ss_pred             CeEEEEecCCCccccccceeeeeEEEEecCCCHHHHHHHHHHhhhhcc--chhhHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            345666665543221   123456688999999999998887664322  223345677888888988766543322   


Q ss_pred             ----HhccC--CHHHHHHHHHHH
Q 039644          170 ----FLHKR--EKEVWESAIDKL  186 (192)
Q Consensus       170 ----~l~~~--~~~~w~~~l~~l  186 (192)
                          .....  +.+...++++.+
T Consensus       212 ~~~~~~~~~~it~~~~~~al~~l  234 (238)
T d1in4a2         212 DMLTVVKADRINTDIVLKTMEVL  234 (238)
T ss_dssp             HHHHHHTCSSBCHHHHHHHHHHH
T ss_pred             HHHHHhcCCccCHHHHHHHHHhh
Confidence                11112  256667777665

>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=95.28  E-value=0.043  Score=37.32  Aligned_cols=106  Identities=9%  Similarity=0.031  Sum_probs=61.3

Q ss_pred             CchhHHHHHHHHHhhCCC---cceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhcCCceEEEEEeCC
Q 039644            1 IGKTAIARAIFDKISGDF---ECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRLSRMKVLIVFDDV   77 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F---~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~LlVlDdv   77 (192)
                      +|||++|..+.+.+...+   +..+++.--+.   . -.+.++. .+.+.+...+.            .+++=++|+|++
T Consensus        26 ~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~~---~-I~Id~IR-~i~~~~~~~~~------------~~~~KviIId~a   88 (198)
T d2gnoa2          26 SYPREVSLELPEYVEKFPPKASDVLEIDPEGE---N-IGIDDIR-TIKDFLNYSPE------------LYTRKYVIVHDC   88 (198)
T ss_dssp             SHHHHHHHHHHHHHHTSCCCTTTEEEECCSSS---C-BCHHHHH-HHHHHHTSCCS------------SSSSEEEEETTG
T ss_pred             CCHHHHHHHHHHHHhccccCCCCEEEEeCCcC---C-CCHHHHH-HHHHHHhhCcc------------cCCCEEEEEeCc
Confidence            599999999998653322   34555541111   0 2344443 34444432211            244458999999


Q ss_pred             CCch--hHHHhhccCCCCCCCceEEEEecchhHH-hhc-CCCceEecCCC
Q 039644           78 TCFS--QLESLMGSLDWLTPVSRIILTTRNKQVL-RNW-GVSKIYEMEAL  123 (192)
Q Consensus        78 ~~~~--~~~~l~~~~~~~~~~~~iivTtR~~~~~-~~~-~~~~~~~l~~l  123 (192)
                      +...  ....+...+-....++.+|++|.+.... ... +....+.+.+.
T Consensus        89 d~l~~~aqNaLLK~LEEPp~~t~fiLit~~~~~ll~TI~SRC~~i~~~~p  138 (198)
T d2gnoa2          89 ERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSRVFRVVVNVP  138 (198)
T ss_dssp             GGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCC
T ss_pred             cccchhhhhHHHHHHhCCCCCceeeeccCChhhCHHHHhcceEEEeCCCc
Confidence            9664  4667766665556778888887765422 222 44566777643

>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=94.86  E-value=0.039  Score=37.44  Aligned_cols=116  Identities=10%  Similarity=0.041  Sum_probs=60.7

Q ss_pred             CchhHHHHHHHHHhhC------CCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhc--CCceEEE
Q 039644            1 IGKTAIARAIFDKISG------DFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRL--SRMKVLI   72 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~------~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l--~~~~~Ll   72 (192)
                      +|||+++..+++++..      --...+|.-+.+..-.......++..              ....+...+  ...+.+|
T Consensus        54 VGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~~~LiAg~~~rG~~E~--------------rl~~il~e~~~~~~~iIL  119 (195)
T d1jbka_          54 VGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEE--------------RLKGVLNDLAKQEGNVIL  119 (195)
T ss_dssp             SCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHHTTTCSHHHHHH--------------HHHHHHHHHHHSTTTEEE
T ss_pred             cccHHHHHHHHHHHHhCCCCHHHcCceEEEeeHHHHhccCCccHHHHH--------------HHHHHHHHHhcCCCcEEE
Confidence            6999999999997532      12345555322221100011111111              122222222  2457899


Q ss_pred             EEeCCCCch----------hHHHhhccCCCCCCCceEEEEecchhHHhhc-------CCCceEecCCCCHHHHHHHH
Q 039644           73 VFDDVTCFS----------QLESLMGSLDWLTPVSRIILTTRNKQVLRNW-------GVSKIYEMEALEYHHALELF  132 (192)
Q Consensus        73 VlDdv~~~~----------~~~~l~~~~~~~~~~~~iivTtR~~~~~~~~-------~~~~~~~l~~l~~~ea~~lf  132 (192)
                      ++|++...-          .-+-+.+++.  .+.-++|.+|..+......       ..-+.+.+...+.+++..++
T Consensus       120 fIDeih~l~~~g~~~g~~d~~~~Lkp~L~--rg~l~~IgatT~eey~~~~e~d~aL~rrF~~I~V~Ep~~e~t~~IL  194 (195)
T d1jbka_         120 FIDELHTMVGAGKADGAMDAGNMLKPALA--RGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             EEETGGGGTT------CCCCHHHHHHHHH--TTSCCEEEEECHHHHHHHTTTCHHHHTTEEEEECCCCCHHHHHTTC
T ss_pred             EcchHHHHhcCCCCCCcccHHHHHHHHHh--CCCceEEecCCHHHHHHHHHcCHHHHhcCCEeecCCCCHHHHHHHh
Confidence            999996431          1123333332  2345677777665554443       22367888888888877653

>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=94.20  E-value=0.75  Score=34.30  Aligned_cols=120  Identities=12%  Similarity=0.041  Sum_probs=59.7

Q ss_pred             CchhHHHHHHHHHhh-C-----CCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCCcCchHHHHhhc-C-CceEEE
Q 039644            1 IGKTAIARAIFDKIS-G-----DFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNVMPYIDLNFRRL-S-RMKVLI   72 (192)
Q Consensus         1 iGKTtLa~~~~~~~~-~-----~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~l-~-~~~~Ll   72 (192)
                      +|||+++..+++++. .     -....+|...++.....-....++              .+.+..+...+ . ..+++|
T Consensus        54 vGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~l~ag~~~~g~~--------------e~r~~~i~~~~~~~~~~~il  119 (387)
T d1qvra2          54 VGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEF--------------EERLKAVIQEVVQSQGEVIL  119 (387)
T ss_dssp             SCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-----------CH--------------HHHHHHHHHHHHTTCSSEEE
T ss_pred             CCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhhhhcccCcchhH--------------HHHHHHHHHHhccCCCceEE
Confidence            799999999988642 1     123566664333211100000011              11222233333 2 347899


Q ss_pred             EEeCCCCchh----------HHHhhccCCCCCCCceEEEEecchhHHhhc------CCCceEecCCCCHHHHHHHHHHhh
Q 039644           73 VFDDVTCFSQ----------LESLMGSLDWLTPVSRIILTTRNKQVLRNW------GVSKIYEMEALEYHHALELFSQHA  136 (192)
Q Consensus        73 VlDdv~~~~~----------~~~l~~~~~~~~~~~~iivTtR~~~~~~~~------~~~~~~~l~~l~~~ea~~lf~~~~  136 (192)
                      ++|++...-.          -+-|.+++.  .+.-++|-+|-........      ..-+.+.+.+.+.+++..++....
T Consensus       120 fide~h~l~~~g~~~g~~d~a~~Lkp~L~--rg~~~~I~~tT~~ey~~~e~d~al~rrF~~v~v~ep~~~~~~~il~~~~  197 (387)
T d1qvra2         120 FIDELHTVVGAGKAEGAVDAGNMLKPALA--RGELRLIGATTLDEYREIEKDPALERRFQPVYVDEPTVEETISILRGLK  197 (387)
T ss_dssp             EECCC-------------------HHHHH--TTCCCEEEEECHHHHHHHTTCTTTCSCCCCEEECCCCHHHHHHHHHHHH
T ss_pred             EeccHHHHhcCCCCCCcccHHHHHHHHHh--CCCcceeeecCHHHHHHhcccHHHHHhcccccCCCCcHHHHHHHHHHHH
Confidence            9999975421          122333332  2334566666554443321      224678899999999999987654

>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=93.38  E-value=0.19  Score=35.91  Aligned_cols=76  Identities=17%  Similarity=0.176  Sum_probs=43.0

Q ss_pred             CchhHHHHHHHHHhh-CCCcceEEEeeccccccCCCChHHHHHHHHHHHhcC--------------CCC--cC------c
Q 039644            1 IGKTAIARAIFDKIS-GDFECSCFLENVREESQRPGGLACLRQKLLSNILKD--------------KNV--MP------Y   57 (192)
Q Consensus         1 iGKTtLa~~~~~~~~-~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~--------------~~~--~~------~   57 (192)
                      +|||+|+.+++.... .+=+..+++. +++-.   ....++..++.+.-...              .++  ..      .
T Consensus        79 ~GKt~l~~~i~~~~~~~~~~v~V~~~-iGer~---~ev~~~~~~~~~~~~~~~~~~~~~tvvv~~~s~~~~~~r~~~~~~  154 (276)
T d2jdid3          79 VGKTVLIMELINNVAKAHGGYSVFAG-VGERT---REGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVALT  154 (276)
T ss_dssp             SSHHHHHHHHHHHHTTTCSSEEEEEE-ESCCH---HHHHHHHHHHHHHTSSCSSSSCCCEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhhCCCeEEEEE-eccCh---HHHHHHHHHHHhcCccccccccceEEEEEECCCCCHHHHHHHHHH
Confidence            699999999998743 3324455554 33311   34566666665531110              011  00      2


Q ss_pred             hHHHHhhc---CCceEEEEEeCCCCc
Q 039644           58 IDLNFRRL---SRMKVLIVFDDVTCF   80 (192)
Q Consensus        58 ~~~l~~~l---~~~~~LlVlDdv~~~   80 (192)
                      .-.+.+++   .+++.|+++||+...
T Consensus       155 a~~iAEyf~~~~G~~VLv~~Dsltr~  180 (276)
T d2jdid3         155 GLTVAEYFRDQEGQDVLLFIDNIFRF  180 (276)
T ss_dssp             HHHHHHHHHHTTCSCEEEEEECTHHH
T ss_pred             HHHHHHHHHhcCCCeEEEEEcchhHH
Confidence            22344444   378999999999644

>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=92.14  E-value=0.18  Score=35.84  Aligned_cols=68  Identities=15%  Similarity=0.091  Sum_probs=38.8

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC---------cCchHHHHhhcCC-ceE
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV---------MPYIDLNFRRLSR-MKV   70 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---------~~~~~~l~~~l~~-~~~   70 (192)
                      +|||+||.+++......=..++|++.-..     ++.     .+++.++.+.+.         .+..+.+....++ ..-
T Consensus        68 sGKT~l~l~~~~~aqk~g~~v~yiDtE~~-----~~~-----~~a~~~Gvd~d~i~~~~~~~~E~~~~~~~~l~~~~~~~  137 (268)
T d1xp8a1          68 GGKTTLALAIVAQAQKAGGTCAFIDAEHA-----LDP-----VYARALGVNTDELLVSQPDNGEQALEIMELLVRSGAID  137 (268)
T ss_dssp             SSHHHHHHHHHHHHHHTTCCEEEEESSCC-----CCH-----HHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTTTCCS
T ss_pred             cchHHHHHHHHHHHHhCCCEEEEEECCcc-----CCH-----HHHHHhCCCchhEEEEcCCCHHHHHHHHHHHHhcCCCc
Confidence            69999999998865443345788873222     333     244444433222         1133333333333 456


Q ss_pred             EEEEeCCC
Q 039644           71 LIVFDDVT   78 (192)
Q Consensus        71 LlVlDdv~   78 (192)
                      |+|+|.+.
T Consensus       138 liIiDSi~  145 (268)
T d1xp8a1         138 VVVVDSVA  145 (268)
T ss_dssp             EEEEECTT
T ss_pred             EEEEeccc
Confidence            99999995

>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=91.49  E-value=0.044  Score=35.73  Aligned_cols=24  Identities=33%  Similarity=0.353  Sum_probs=18.0

Q ss_pred             CchhHHHHHHHHHhhCCC-cceEEE
Q 039644            1 IGKTAIARAIFDKISGDF-ECSCFL   24 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F-~~~~wv   24 (192)
                      +||||+|+.++.++...| +...++
T Consensus        17 sGKTTia~~La~~L~~~~~~~~~~~   41 (183)
T d1m8pa3          17 SGKDAIARALQVTLNQQGGRSVSLL   41 (183)
T ss_dssp             SSHHHHHHHHHHHHHHHCSSCEEEE
T ss_pred             CCHHHHHHHHHHHHhhcCCCchhhh
Confidence            699999999999876544 444444

>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=91.36  E-value=0.36  Score=34.21  Aligned_cols=69  Identities=14%  Similarity=0.143  Sum_probs=39.8

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHhcCCCC---c------CchHHHHhhc-CCceE
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNILKDKNV---M------PYIDLNFRRL-SRMKV   70 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---~------~~~~~l~~~l-~~~~~   70 (192)
                      +|||+||.+++......-...+|++.-..     ++..     .+++++.+.+.   .      +..+.+.... .+..-
T Consensus        71 ~GKT~l~l~~~~~~q~~g~~~vyIDtE~~-----~~~e-----~a~~~GvD~d~il~~~~~~~E~~~~~~~~l~~~~~~~  140 (269)
T d1mo6a1          71 SGKTTVALHAVANAQAAGGVAAFIDAEHA-----LDPD-----YAKKLGVDTDSLLVSQPDTGEQALEIADMLIRSGALD  140 (269)
T ss_dssp             SSHHHHHHHHHHHHHHTTCEEEEEESSCC-----CCHH-----HHHHHTCCGGGCEEECCSSHHHHHHHHHHHHHTTCEE
T ss_pred             cHHHHHHHHHHHHHhcCCCEEEEEECCcc-----CCHH-----HHHHhCCCHHHeEEecCCCHHHHHHHHHHHHhcCCCC
Confidence            69999999998866555567899973222     3322     23444433222   1      1222222223 34577


Q ss_pred             EEEEeCCCC
Q 039644           71 LIVFDDVTC   79 (192)
Q Consensus        71 LlVlDdv~~   79 (192)
                      |+|+|.+..
T Consensus       141 liIiDSi~a  149 (269)
T d1mo6a1         141 IVVIDSVAA  149 (269)
T ss_dssp             EEEEECSTT
T ss_pred             EEEEecccc
Confidence            999999953

>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=91.36  E-value=0.032  Score=36.59  Aligned_cols=15  Identities=13%  Similarity=0.286  Sum_probs=13.2

Q ss_pred             CchhHHHHHHHHHhh
Q 039644            1 IGKTAIARAIFDKIS   15 (192)
Q Consensus         1 iGKTtLa~~~~~~~~   15 (192)
                      +||||||+.+++++.
T Consensus        18 sGKTTla~~La~~~~   32 (192)
T d1lw7a2          18 SGKSVLVNKLAAVFN   32 (192)
T ss_dssp             SHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHhC
Confidence            699999999999764

>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=91.34  E-value=0.037  Score=36.78  Aligned_cols=25  Identities=20%  Similarity=0.133  Sum_probs=19.5

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +||||+|+.++.++...|....++.
T Consensus        30 SGKTTiAk~La~~l~~~~~~~~~~~   54 (195)
T d1x6va3          30 AGKTTVSMALEEYLVCHGIPCYTLD   54 (195)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             CCHHHHHHHHHHHHHhcCCCccchh
Confidence            5999999999998876666555553

>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=91.30  E-value=0.038  Score=35.35  Aligned_cols=15  Identities=27%  Similarity=0.594  Sum_probs=13.5

Q ss_pred             CchhHHHHHHHHHhh
Q 039644            1 IGKTAIARAIFDKIS   15 (192)
Q Consensus         1 iGKTtLa~~~~~~~~   15 (192)
                      +||||+|+.++.++.
T Consensus        13 sGKSTvak~La~~L~   27 (169)
T d1kaga_          13 AGKSTIGRQLAQQLN   27 (169)
T ss_dssp             SCHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHhC
Confidence            699999999999874

>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=90.86  E-value=0.058  Score=34.88  Aligned_cols=18  Identities=17%  Similarity=0.313  Sum_probs=15.2

Q ss_pred             CchhHHHHHHHHHhhCCC
Q 039644            1 IGKTAIARAIFDKISGDF   18 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F   18 (192)
                      +|||||++++...+..+.
T Consensus        13 SGKTTL~~~L~~~l~~~g   30 (170)
T d1np6a_          13 TGKTTLLKKLIPALCARG   30 (170)
T ss_dssp             SCHHHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHHHHCC
Confidence            699999999999876553

>d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: ATP:corrinoid adenosyltransferase CobA
species: Salmonella typhimurium [TaxId: 90371]

Probab=90.41  E-value=0.29  Score=31.78  Aligned_cols=62  Identities=19%  Similarity=0.208  Sum_probs=33.0

Q ss_pred             HHhhcCCceE-EEEEeCCCCch-----hHHHhhccCCCCCCCceEEEEecchhHHhhcCCCceEecCC
Q 039644           61 NFRRLSRMKV-LIVFDDVTCFS-----QLESLMGSLDWLTPVSRIILTTRNKQVLRNWGVSKIYEMEA  122 (192)
Q Consensus        61 l~~~l~~~~~-LlVlDdv~~~~-----~~~~l~~~~~~~~~~~~iivTtR~~~~~~~~~~~~~~~l~~  122 (192)
                      .+..+.+..| |+|||.+..--     ..+.+...+.....+..+|+|-|+..-.-..-...+.+|..
T Consensus        86 a~~~~~~~~~dllILDEi~~Ai~~gli~~~~v~~ll~~rp~~~evVlTGr~~p~~L~e~ADlVTEm~~  153 (157)
T d1g5ta_          86 GKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILDLADTVSELRP  153 (157)
T ss_dssp             HHHHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHHHHCSEEEECCC
T ss_pred             HHHHhhcCccCEEeHHHHHHHHHcCCCCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhcceeeeeee
Confidence            4445555555 99999984211     12222222333345678999999855332222334444443

>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=89.64  E-value=0.2  Score=36.47  Aligned_cols=15  Identities=27%  Similarity=0.538  Sum_probs=12.7

Q ss_pred             CchhHHHHHHHHHhh
Q 039644            1 IGKTAIARAIFDKIS   15 (192)
Q Consensus         1 iGKTtLa~~~~~~~~   15 (192)
                      +|||.+|+.+++.+-
T Consensus        64 ~GKt~lak~la~~l~   78 (315)
T d1qvra3          64 VGKTELAKTLAATLF   78 (315)
T ss_dssp             SSHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHhc
Confidence            699999999998763

>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=89.29  E-value=0.52  Score=33.47  Aligned_cols=77  Identities=14%  Similarity=0.165  Sum_probs=40.1

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEeeccccccCCCChHHHHHHHHHHHh--------cCCCC--cC------chHHHHhh
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLENVREESQRPGGLACLRQKLLSNIL--------KDKNV--MP------YIDLNFRR   64 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~l~~~~~--------~~~~~--~~------~~~~l~~~   64 (192)
                      +|||+|+.+.......+-..++++- +.+..   ....++..++...-.        ...++  ..      ..-.+.++
T Consensus        78 ~GKt~l~~~~~~~~~~~~~v~V~~~-iGer~---~Ev~e~~~~~~~~~~~~~tvvv~~tsd~p~~~r~~a~~~a~tiAEy  153 (276)
T d1fx0a3          78 TGKTAVATDTILNQQGQNVICVYVA-IGQKA---SSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLAPYTGAALAEY  153 (276)
T ss_dssp             SSHHHHHHHHHHTCCTTTCEEEEEE-ESCCH---HHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHhhhcccCceeeeee-ecchh---HHHHHHHHhhccCCcceeeeecccccCccHHHHHHHHHHHHHHHHH
Confidence            6999999987765555545556664 22211   234444444433210        00011  11      11223333


Q ss_pred             c--CCceEEEEEeCCCCch
Q 039644           65 L--SRMKVLIVFDDVTCFS   81 (192)
Q Consensus        65 l--~~~~~LlVlDdv~~~~   81 (192)
                      +  .+++.|+++||+....
T Consensus       154 frd~G~~Vlll~Dsltr~A  172 (276)
T d1fx0a3         154 FMYRERHTLIIYDDLSKQA  172 (276)
T ss_dssp             HHHTTCEEEEEEECHHHHH
T ss_pred             HHHcCCceeEEeeccHHHH
Confidence            3  4789999999996543

>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=88.72  E-value=0.089  Score=34.06  Aligned_cols=16  Identities=25%  Similarity=0.453  Sum_probs=13.8

Q ss_pred             CchhHHHHHHHHHhhC
Q 039644            1 IGKTAIARAIFDKISG   16 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~   16 (192)
                      +||||+|+.+++++..
T Consensus        14 sGKsTva~~L~~~l~~   29 (178)
T d1qhxa_          14 AGKSGIVRCLQSVLPE   29 (178)
T ss_dssp             SSHHHHHHHHHHHSSS
T ss_pred             CCHHHHHHHHHHHcCC
Confidence            6999999999998753

>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=88.31  E-value=0.15  Score=33.54  Aligned_cols=24  Identities=21%  Similarity=0.347  Sum_probs=17.8

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEE
Q 039644            1 IGKTAIARAIFDKISGDFECSCFL   24 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv   24 (192)
                      +||||||+.+...+...+.....+
T Consensus        33 SGKSTla~~L~~~l~~~~~~~~~~   56 (198)
T d1rz3a_          33 SGKTTLANQLSQTLREQGISVCVF   56 (198)
T ss_dssp             SSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCHHHHHHHHHHHhccccccceec
Confidence            699999999998776555444444

>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=87.67  E-value=0.1  Score=33.62  Aligned_cols=15  Identities=13%  Similarity=0.490  Sum_probs=12.9

Q ss_pred             CchhHHHHHHHHHhh
Q 039644            1 IGKTAIARAIFDKIS   15 (192)
Q Consensus         1 iGKTtLa~~~~~~~~   15 (192)
                      +||||+|+.++..+.
T Consensus        13 sGKTTva~~L~~~~~   27 (176)
T d2bdta1          13 VGKSTTCKRLAAQLD   27 (176)
T ss_dssp             SSHHHHHHHHHHHSS
T ss_pred             CCHHHHHHHHHHHcC
Confidence            699999999998753

>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=87.19  E-value=0.14  Score=33.27  Aligned_cols=17  Identities=24%  Similarity=0.380  Sum_probs=14.5

Q ss_pred             CchhHHHHHHHHHhhCC
Q 039644            1 IGKTAIARAIFDKISGD   17 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~   17 (192)
                      +||||+++.+++++.-.
T Consensus        12 ~GKSTig~~La~~l~~~   28 (165)
T d2iyva1          12 SGKSTIGRRLAKALGVG   28 (165)
T ss_dssp             SSHHHHHHHHHHHHTCC
T ss_pred             CCHHHHHHHHHHHhCCC
Confidence            69999999999987543

>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=87.10  E-value=0.12  Score=33.51  Aligned_cols=17  Identities=18%  Similarity=0.212  Sum_probs=14.8

Q ss_pred             CchhHHHHHHHHHhhCC
Q 039644            1 IGKTAIARAIFDKISGD   17 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~   17 (192)
                      +|||||+.++..+++.+
T Consensus        12 SGKTTli~~l~~~L~~~   28 (165)
T d1xjca_          12 SGKTTLMEKWVAAAVRE   28 (165)
T ss_dssp             SSHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHhC
Confidence            69999999999987655

>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=87.03  E-value=0.12  Score=37.15  Aligned_cols=27  Identities=22%  Similarity=0.327  Sum_probs=18.1

Q ss_pred             CchhHHHHHHHHHhhC-CCcceEEEeec
Q 039644            1 IGKTAIARAIFDKISG-DFECSCFLENV   27 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~-~F~~~~wv~~~   27 (192)
                      +|||+|+.++++.... +-.+++.+..+
T Consensus        54 ~GKT~l~~~i~~~~~~~~~~~v~~~~~i   81 (289)
T d1xpua3          54 AGKTMLLQNIAQSIAYNHPDCVLMVLLI   81 (289)
T ss_dssp             SSHHHHHHHHHHHHHHHCTTSEEEEEEE
T ss_pred             CCHHHHHHHHHHHHhhcCCCeEEEEEee
Confidence            6999999999996543 33445554433

>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=86.85  E-value=0.69  Score=31.15  Aligned_cols=24  Identities=17%  Similarity=0.279  Sum_probs=17.5

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEE
Q 039644            1 IGKTAIARAIFDKISGDFECSCFL   24 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv   24 (192)
                      +||||+++.+++.+..+--.+..+
T Consensus        14 sGKsT~~~~L~~~L~~~g~~v~~~   37 (209)
T d1nn5a_          14 AGKSTQSRKLVEALCAAGHRAELL   37 (209)
T ss_dssp             SSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCHHHHHHHHHHHHHHCCCcEEEE
Confidence            699999999999876553333444

>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=86.84  E-value=0.12  Score=33.26  Aligned_cols=14  Identities=29%  Similarity=0.582  Sum_probs=12.7

Q ss_pred             CchhHHHHHHHHHh
Q 039644            1 IGKTAIARAIFDKI   14 (192)
Q Consensus         1 iGKTtLa~~~~~~~   14 (192)
                      +||||+|+.+++++
T Consensus        15 sGKTTia~~La~~l   28 (173)
T d1rkba_          15 VGKTTLGKELASKS   28 (173)
T ss_dssp             SSHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH
Confidence            69999999999876

>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=86.54  E-value=0.22  Score=32.19  Aligned_cols=17  Identities=18%  Similarity=0.382  Sum_probs=14.2

Q ss_pred             CchhHHHHHHHHHhhCC
Q 039644            1 IGKTAIARAIFDKISGD   17 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~   17 (192)
                      +|||||+++++..+...
T Consensus        12 tGKTtl~~~i~~~l~~~   28 (189)
T d2i3ba1          12 VGKTTLIHKASEVLKSS   28 (189)
T ss_dssp             SCHHHHHHHHHHHHHHT
T ss_pred             CcHHHHHHHHHHHHHHC
Confidence            69999999999976544

>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=86.48  E-value=0.15  Score=34.14  Aligned_cols=17  Identities=24%  Similarity=0.159  Sum_probs=14.0

Q ss_pred             CchhHHHHHHHHHhhCC
Q 039644            1 IGKTAIARAIFDKISGD   17 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~   17 (192)
                      +||||+|+++++.+...
T Consensus        13 sGKSTla~~L~~~l~~~   29 (213)
T d1bifa1          13 RGKTYISKKLTRYLNFI   29 (213)
T ss_dssp             SSHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHhc
Confidence            69999999999876533

>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=86.41  E-value=0.15  Score=32.22  Aligned_cols=13  Identities=38%  Similarity=0.521  Sum_probs=11.1

Q ss_pred             CchhHHHHHHHHH
Q 039644            1 IGKTAIARAIFDK   13 (192)
Q Consensus         1 iGKTtLa~~~~~~   13 (192)
                      +||||||+++..+
T Consensus        13 sGKTTla~~L~~~   25 (152)
T d1ly1a_          13 SGKSTWAREFIAK   25 (152)
T ss_dssp             SSHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHh
Confidence            6999999988764

>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=85.87  E-value=0.15  Score=32.81  Aligned_cols=15  Identities=27%  Similarity=0.501  Sum_probs=13.3

Q ss_pred             CchhHHHHHHHHHhh
Q 039644            1 IGKTAIARAIFDKIS   15 (192)
Q Consensus         1 iGKTtLa~~~~~~~~   15 (192)
                      +||||+|+.++.++.
T Consensus        17 sGKsT~a~~La~~l~   31 (171)
T d1knqa_          17 SGKSAVASEVAHQLH   31 (171)
T ss_dssp             SCHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHhC
Confidence            699999999999863

>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=85.73  E-value=0.32  Score=31.61  Aligned_cols=25  Identities=8%  Similarity=0.189  Sum_probs=18.3

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +||||+++.+++.+..+......++
T Consensus        12 sGKTT~~~~La~~L~~~~~~~~~~~   36 (194)
T d1nksa_          12 VGKSTVLAKVKEILDNQGINNKIIN   36 (194)
T ss_dssp             SCHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             CCHHHHHHHHHHHHHHcCCCEEEEE
Confidence            6999999999998865544444443

>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=85.19  E-value=0.2  Score=34.86  Aligned_cols=18  Identities=39%  Similarity=0.730  Sum_probs=15.0

Q ss_pred             CchhHHHHHHHHHhhCCC
Q 039644            1 IGKTAIARAIFDKISGDF   18 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F   18 (192)
                      +|||+||+.++..+...|
T Consensus        43 tGKT~la~~la~~~~~~~   60 (273)
T d1gvnb_          43 SGKTSLRSAIFEETQGNV   60 (273)
T ss_dssp             SCTHHHHHHHHHHTTTCC
T ss_pred             CCHHHHHHHHHHHhhcce
Confidence            699999999999875543

>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=83.96  E-value=0.41  Score=32.67  Aligned_cols=25  Identities=16%  Similarity=0.286  Sum_probs=22.1

Q ss_pred             CchhHHHHHHHHHhhCCCcceEEEe
Q 039644            1 IGKTAIARAIFDKISGDFECSCFLE   25 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F~~~~wv~   25 (192)
                      +|||+||.+++.....+...++|++
T Consensus        37 sGKT~l~~qia~~~~~~~~~~~~is   61 (242)
T d1tf7a2          37 TGKTLLVSRFVENACANKERAILFA   61 (242)
T ss_dssp             SSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             CCHHHHHHHHHHHHHHhccccceee
Confidence            6999999999998877778888887

>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=83.71  E-value=0.22  Score=32.36  Aligned_cols=15  Identities=20%  Similarity=0.412  Sum_probs=13.4

Q ss_pred             CchhHHHHHHHHHhh
Q 039644            1 IGKTAIARAIFDKIS   15 (192)
Q Consensus         1 iGKTtLa~~~~~~~~   15 (192)
                      +||||+|+.+++++.
T Consensus        13 sGKSTia~~LA~~Lg   27 (170)
T d1e6ca_          13 CGMTTVGRELARALG   27 (170)
T ss_dssp             SSHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHhC
Confidence            699999999999874

>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=83.67  E-value=0.29  Score=31.64  Aligned_cols=17  Identities=24%  Similarity=0.638  Sum_probs=14.1

Q ss_pred             CchhHHHHHHHHHhhCC
Q 039644            1 IGKTAIARAIFDKISGD   17 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~   17 (192)
                      +|||||++.++..+...
T Consensus        11 ~GKSTLl~~i~~~l~~~   27 (178)
T d1ye8a1          11 VGKTTLVKKIVERLGKR   27 (178)
T ss_dssp             SSHHHHHHHHHHHHGGG
T ss_pred             cHHHHHHHHHHhcCCCC
Confidence            69999999999976543

>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=82.94  E-value=0.48  Score=30.51  Aligned_cols=18  Identities=17%  Similarity=0.331  Sum_probs=15.4

Q ss_pred             CchhHHHHHHHHHhhCCC
Q 039644            1 IGKTAIARAIFDKISGDF   18 (192)
Q Consensus         1 iGKTtLa~~~~~~~~~~F   18 (192)
                      +||||+++.+..++....
T Consensus        12 sGKsT~~~~L~~~l~~~~   29 (190)
T d1khta_          12 VGSTTSSQLAMDNLRKEG   29 (190)
T ss_dssp             SCHHHHHHHHHHHHHTTT
T ss_pred             CCHHHHHHHHHHHHHHcC
Confidence            699999999999876554

>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=82.94  E-value=0.19  Score=32.42  Aligned_cols=14  Identities=36%  Similarity=0.413  Sum_probs=11.9

Q ss_pred             CchhHHHHHHHHHh
Q 039644            1 IGKTAIARAIFDKI   14 (192)
Q Consensus         1 iGKTtLa~~~~~~~   14 (192)
                      +||||+|+.+++++
T Consensus        15 sGKSTia~~La~~l   28 (176)
T d1zp6a1          15 SGKSTIAEALANLP   28 (176)
T ss_dssp             SCHHHHHHHHHTCS
T ss_pred             CCHHHHHHHHHHHh
Confidence            69999999998754

>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=82.49  E-value=0.27  Score=31.57  Aligned_cols=15  Identities=33%  Similarity=0.519  Sum_probs=12.9

Q ss_pred             CchhHHHHHHHHHhh
Q 039644            1 IGKTAIARAIFDKIS   15 (192)
Q Consensus         1 iGKTtLa~~~~~~~~   15 (192)
                      +||||+|+.+++++.
T Consensus        16 sGKTT~~~~La~~l~   30 (174)
T d1y63a_          16 TGKTSMAEMIAAELD   30 (174)
T ss_dssp             SSHHHHHHHHHHHST
T ss_pred             CCHHHHHHHHHHHhC
Confidence            699999999998753

>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=80.96  E-value=0.32  Score=31.29  Aligned_cols=14  Identities=36%  Similarity=0.636  Sum_probs=13.1

Q ss_pred             CchhHHHHHHHHHh
Q 039644            1 IGKTAIARAIFDKI   14 (192)
Q Consensus         1 iGKTtLa~~~~~~~   14 (192)
                      +||||+++.+++++
T Consensus        11 sGKsTi~k~La~~l   24 (161)
T d1viaa_          11 SGKSTLARALAKDL   24 (161)
T ss_dssp             SCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHh
Confidence            69999999999987