RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

Searching..................................................done

Query= 537021.9.peg.472_1
         (369 letters)



>gnl|CDD|32641 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
           replication, recombination, and repair].
          Length = 515

 Score =  353 bits (906), Expect = 5e-98
 Identities = 153/356 (42%), Positives = 220/356 (61%), Gaps = 5/356 (1%)

Query: 1   MIGQKPMIKTLTNAFKSGRIAQSYMLSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFE 60
           ++GQ+ ++KTL+NA ++GRIA +Y+ SG RG+GKTT ARI+A++LN +      PT E  
Sbjct: 18  VVGQEHVVKTLSNALENGRIAHAYLFSGPRGVGKTTIARILAKALNCENG----PTAEPC 73

Query: 61  GFGEHCQAIIRGNHVDVVELDAASHTSIDDVREIIDQIYYKPISARFRVYIMDEVQMLST 120
           G    C+ I  G+ +DV+E+DAAS+T +DD+REII+++ Y P   R++VYI+DEV MLS 
Sbjct: 74  GKCISCKEINEGSLIDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHMLSK 133

Query: 121 AAFNGLLKTLEEPPPHVKFIFATTEIRKIPITVLSRCQRFDLHRISIGDLIELFTKILQE 180
            AFN LLKTLEEPP HVKFI ATTE +KIP T+LSRCQRFD  R+ + ++ +    IL +
Sbjct: 134 QAFNALLKTLEEPPSHVKFILATTEPQKIPNTILSRCQRFDFKRLDLEEIAKHLAAILDK 193

Query: 181 ESIEFDPEAVAMIARASDGSARDGLSLLDQAIARCNDKIVTSSVRLMLALADRNRIMDLF 240
           E I  + +A+++IARA++GS RD LSLLDQAIA    +I   SVR ML L D  +++ L 
Sbjct: 194 EGINIEEDALSLIARAAEGSLRDALSLLDQAIAFGEGEITLESVRDMLGLTDIEKLLSLL 253

Query: 241 GYLIKGDIINVLQEFSSQYDSGVNPSVILHDLAEFTHLVTRIKYIPEMADTLLYSEAENA 300
             ++KGD    L+  +   + G +P   L DL  F   +   K        L  +E E  
Sbjct: 254 EAILKGDAKEALRLINELIEEGKDPEAFLEDLLNFLRDLLLFKQTVPNELQLNTTEIEER 313

Query: 301 RALQYSKEVSITFLSRFWQMILKGISEIEGFSRPMEAVEMVLIRLAHAVQLPSPEE 356
                + ++S+  L R +Q++L G+ E++    P   +EM LIRL  A        
Sbjct: 314 TKEL-ASQISVLNLQRLYQLLLPGLKELKRSLSPRLGLEMTLIRLLEAAPASDAAS 368


>gnl|CDD|36207 KOG0989, KOG0989, KOG0989, Replication factor C, subunit RFC4
           [Replication, recombination and repair].
          Length = 346

 Score =  130 bits (327), Expect = 8e-31
 Identities = 69/276 (25%), Positives = 125/276 (45%), Gaps = 16/276 (5%)

Query: 1   MIGQKPMIKTLTNAFKSGRIAQSYMLSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFE 60
           + GQ+ +++ L NA    RI   Y+  G  G GKT+TA   AR+LN          +   
Sbjct: 38  LAGQEHVVQVLKNALL-RRILPHYLFYGPPGTGKTSTALAFARALN-------CEQLFPC 89

Query: 61  GFGEHCQAIIRGNHVDVVELDAASHTSIDDVREIIDQIYYKPISARFRVYIMDEVQMLST 120
              E   +  RG  V   ++   +  ++   R              F++ I+DE   +++
Sbjct: 90  RVLELNASDERGISVVREKIKNFAKLTVLLKRSD------GYPCPPFKIIILDECDSMTS 143

Query: 121 AAFNGLLKTLEEPPPHVKFIFATTEIRKIPITVLSRCQRFDLHRISIGDLIELFTKILQE 180
            A   L +T+E+     +FI     + +I   ++SRCQ+F   ++   D+++   KI  +
Sbjct: 144 DAQAALRRTMEDFSRTTRFILICNYLSRIIRPLVSRCQKFRFKKLKDEDIVDRLEKIASK 203

Query: 181 ESIEFDPEAVAMIARASDGSARDGLSLLDQAIARCNDKIVTSSVRLMLA-LADRNRIMDL 239
           E ++ D +A+ +IA+ SDG  R  ++ L    +    +I TS V   LA +    +++DL
Sbjct: 204 EGVDIDDDALKLIAKISDGDLRRAITTLQSL-SLLGKRITTSLVNEELAGVVPDEKLLDL 262

Query: 240 FGYLIKGDIINVLQEFSSQYDSGVNPSVILHDLAEF 275
               +  D  N ++       SG +P  ++  LAE 
Sbjct: 263 LELALSADTPNTVKRVREIMRSGYSPLQLMSQLAEV 298


>gnl|CDD|73174 COG0470, HolB, ATPase involved in DNA replication [DNA replication,
           recombination, and repair].
          Length = 325

 Score =  102 bits (254), Expect = 2e-22
 Identities = 72/295 (24%), Positives = 121/295 (41%), Gaps = 11/295 (3%)

Query: 3   GQKPMIKTLTNAFKSGRIAQSYMLSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFEGF 62
            Q+ + + L  A +SGR+  + +  G  G+GKTT A  +A+ L  +     +P     G 
Sbjct: 6   WQEAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLP----CGH 61

Query: 63  GEHCQAIIRGNHVDVVELDAA----SHTSIDDVREIIDQIYYKPISARFRVYIMDEVQML 118
              C+ I  GNH D +EL+ +        ++ VRE+ + +   P+   ++V I+DE   L
Sbjct: 62  CRSCKLIPAGNHPDFLELNPSDLRKIDIIVEQVRELAEFLSESPLEGGYKVVIIDEADKL 121

Query: 119 STAAFNGLLKTLEEPPPHVKFIFATTEIRKIPITVLSRCQRFDLHRISIGDLIELFTKIL 178
           +  A N LLKTLEEPP + +FI  T +  KI  T+ SRCQR      S  + I       
Sbjct: 122 TEDAANALLKTLEEPPKNTRFILITNDPSKILPTIRSRCQRIRFKPPSRLEAIAWLEDQG 181

Query: 179 QEESIEFDPEAVAMIARASDGSARDGLSLLDQAIARCNDKIVTSSVRLMLALADRNRIMD 238
            EE               +   A   L + +++I       +  S+  + AL       +
Sbjct: 182 LEEIAAV--AEGDARKAINPLQALAALEIGEESIYEALLLALPESLAQLAALELLKLAEN 239

Query: 239 LFGY-LIKGDIINVLQEFSSQYDSGVNPSVILHDLAEFTHLVTRIKYIPEMADTL 292
            F   L K  ++ +L+    +         +L             + +  +A   
Sbjct: 240 KFLEALEKLWLLLLLEGLLGEDLLDQLQRELLKLDKALIQEEKAAELLDALAQAR 294


>gnl|CDD|32437 COG2256, MGS1, ATPase related to the helicase subunit of the
           Holliday junction resolvase [DNA replication,
           recombination, and repair].
          Length = 436

 Score = 83.0 bits (205), Expect = 1e-16
 Identities = 66/250 (26%), Positives = 105/250 (42%), Gaps = 44/250 (17%)

Query: 1   MIGQKPMI---KTLTNAFKSGRIAQSYMLSGTRGIGKTTTARIIARSLNYKTAHIDVPTV 57
           ++GQ+ ++   K L  A ++G +  S +L G  G GKTT AR+IA + N           
Sbjct: 26  VVGQEHLLGEGKPLRRAVEAGHLH-SMILWGPPGTGKTTLARLIAGTTNA---------- 74

Query: 58  EFEGFGEHCQAIIRGNHVDVVELDAASHTSIDDVREIIDQIYYKPISARFRVYIMDEVQM 117
                                 L A +   + D+REII++     +  R  +  +DE+  
Sbjct: 75  ------------------AFEALSAVTS-GVKDLREIIEEARKNRLLGRRTILFLDEIHR 115

Query: 118 LSTAAFNGLLKTLEEPPPHVKFIFATTEIRKIPIT--VLSRCQRFDLHRISIGDLIELFT 175
            + A  + LL  +E     +  I ATTE     +   +LSR + F+L  +S  D+ +L  
Sbjct: 116 FNKAQQDALLPHVENG--TIILIGATTENPSFELNPALLSRARVFELKPLSSEDIKKLLK 173

Query: 176 KILQEES-------IEFDPEAVAMIARASDGSARDGLSLLDQAIARCNDKIVTSSVRLML 228
           + L +E        I  D EA+  + R S+G AR  L+LL+ A        V     L  
Sbjct: 174 RALLDEERGLGGQIIVLDEEALDYLVRLSNGDARRALNLLELAALSAEPDEVLILELLEE 233

Query: 229 ALADRNRIMD 238
            L  R+   D
Sbjct: 234 ILQRRSARFD 243


>gnl|CDD|36209 KOG0991, KOG0991, KOG0991, Replication factor C, subunit RFC2
           [Replication, recombination and repair].
          Length = 333

 Score = 69.6 bits (170), Expect = 1e-12
 Identities = 58/278 (20%), Positives = 112/278 (40%), Gaps = 34/278 (12%)

Query: 1   MIGQKPMIKTLTNAFKSGRIAQSYMLSGTRGIGKTTTARIIARSL---NYKTAHIDVPTV 57
           ++G +  ++ L+   K G +    ++SG  G GKTT+   +AR L   +YK A       
Sbjct: 29  IVGNEDTVERLSVIAKEGNMPN-LIISGPPGTGKTTSILCLARELLGDSYKEA------- 80

Query: 58  EFEGFGEHCQAIIRGNHVDVVELDAASHTSIDDVREIIDQIYYKPIS---ARFRVYIMDE 114
                              V+EL+A+    ID VR  I     K ++    R ++ I+DE
Sbjct: 81  -------------------VLELNASDERGIDVVRNKIKMFAQKKVTLPPGRHKIIILDE 121

Query: 115 VQMLSTAAFNGLLKTLEEPPPHVKFIFATTEIRKIPITVLSRCQRFDLHRISIGDLIELF 174
              ++  A   L +T+E      +F  A  +  KI   + SRC      ++S   +++  
Sbjct: 122 ADSMTAGAQQALRRTMEIYSNTTRFALACNQSEKIIEPIQSRCAILRYSKLSDQQILKRL 181

Query: 175 TKILQEESIEFDPEAVAMIARASDGSARDGLSLLDQAIARCNDKIVTSSVRLMLALADRN 234
            ++ + E + +  + +  I   + G  R  L+ L Q+       +   +V  +       
Sbjct: 182 LEVAKAEKVNYTDDGLEAIIFTAQGDMRQALNNL-QSTVNGFGLVNQENVFKVCDEPHPL 240

Query: 235 RIMDLFGYLIKGDIINVLQEFSSQYDSGVNPSVILHDL 272
            +  +    +K +I   L+  +  +  G +P  I+  L
Sbjct: 241 LVKKMLQACLKRNIDEALKILAELWKLGYSPEDIITTL 278


>gnl|CDD|36208 KOG0990, KOG0990, KOG0990, Replication factor C, subunit RFC5
           [Replication, recombination and repair].
          Length = 360

 Score = 65.4 bits (159), Expect = 2e-11
 Identities = 63/307 (20%), Positives = 115/307 (37%), Gaps = 41/307 (13%)

Query: 1   MIGQKPMIKTLTNAFKSGRIAQSYMLSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFE 60
           +I Q+P+  T         +       G  G GKT+T    AR                 
Sbjct: 43  VIKQEPIWSTENRYSGMPGLPHLL-FYGPPGTGKTSTILANARDF--------------- 86

Query: 61  GFGEHCQAIIRGNHVDVVELDAASHTSIDDVREII------DQIYYKPISARFRVYIMDE 114
            +  H    +      ++EL+A+    ID VR+ I       Q       A F++ I+DE
Sbjct: 87  -YSPHPTTSM------LLELNASDDRGIDPVRQQIHLFASTQQPTTYSTHAAFKLVILDE 139

Query: 115 VQMLSTAAFNGLLKTLEEPPPHVKFIFATTEIRKIPITVLSRCQRFDLHRISIGDLIELF 174
              ++  A N L + +E+   + +F   +   +KI     SRC RF    +++    E  
Sbjct: 140 ADAMTRDAQNALRRVIEKYTANTRFATISNPPQKIHPAQQSRCTRFRFAPLTMAQQTERQ 199

Query: 175 TKILQEESIEFDPEAVAMIARASDGSARDGLSLLDQAIARCNDKIVTSS-----VRLMLA 229
           + I + E  E +PE  + + R S G  R  L+ L Q+I +   +    +     V     
Sbjct: 200 SHIRESEQKETNPEGYSALGRLSVGDMRVALNYL-QSILKKVMERKELNNPNDLVYQCKG 258

Query: 230 LADRNRIMDLFGYLIKGDIINVLQEFSS-QYDSGVNPSVILHDLAEFTHLV-----TRIK 283
               + I  +    + G+ I ++ + S  +   G+       +L +   +V         
Sbjct: 259 APQPSDIRQIIEKRMNGEDIELMLDDSELKKPKGLARQDRRAELEQRFAIVISKTPVEGH 318

Query: 284 YIPEMAD 290
            + ++AD
Sbjct: 319 ILYQLAD 325


>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
           cellular Activities) superfamily represents an ancient
           group of ATPases belonging to the ASCE (for additional
           strand, catalytic E) division of the P-loop NTPase fold.
           The ASCE division also includes ABC, RecA-like,
           VirD4-like, PilT-like, and SF1/2 helicases. Members of
           the AAA+ ATPases function as molecular chaperons, ATPase
           subunits of proteases, helicases, or nucleic-acid
           stimulated ATPases. The AAA+ proteins contain several
           distinct features in addition to the conserved
           alpha-beta-alpha core domain structure and the Walker A
           and B motifs of the P-loop NTPases..
          Length = 151

 Score = 54.1 bits (130), Expect = 7e-08
 Identities = 37/171 (21%), Positives = 58/171 (33%), Gaps = 39/171 (22%)

Query: 2   IGQKPMIKTLTNAFKSGRIAQSYMLSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFEG 61
           +GQ+  I+ L  A +     ++ +L G  G GKTT AR IA  L                
Sbjct: 1   VGQEEAIEALREALEL-PPPKNLLLYGPPGTGKTTLARAIANELFRP------------- 46

Query: 62  FGEHCQAIIRGNHVDVVELDAASHTSIDDVREIIDQIYYKPISARFR-----VYIMDEVQ 116
                           + L+A+       V E+      + +          V  +DE+ 
Sbjct: 47  ------------GAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEID 94

Query: 117 MLSTAAFNGLLKTLEE------PPPHVKFIFATT--EIRKIPITVLSRCQR 159
            LS  A N LL+ LE          +V+ I AT    +  +   +  R   
Sbjct: 95  SLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDI 145


>gnl|CDD|37239 KOG2028, KOG2028, KOG2028, ATPase related to the helicase subunit
           of the Holliday junction resolvase [Replication,
           recombination and repair].
          Length = 554

 Score = 50.5 bits (120), Expect = 7e-07
 Identities = 53/220 (24%), Positives = 91/220 (41%), Gaps = 45/220 (20%)

Query: 10  TLTNAFKSGRIAQSYMLSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFEGFGEHCQAI 69
            L +  +  RI  S +L G  G GKTT AR+IA     K       +  F          
Sbjct: 152 LLRSLIEQNRI-PSMILWGPPGTGKTTLARLIAS--TSKK-----HSYRF---------- 193

Query: 70  IRGNHVDVVELDAASHTSIDDVREIIDQIY-YKPISARFRVYIMDEVQMLSTAAFNGLLK 128
                   VEL A +    +DVR+I +Q    K ++ R  +  +DE+   + +  +  L 
Sbjct: 194 --------VELSATN-AKTNDVRDIFEQAQNEKSLTKRKTILFIDEIHRFNKSQQDTFLP 244

Query: 129 TLEEPPPHVKFIFATTEIRKIPIT--VLSRCQRFDLHRISIGDLIELFTKI--------- 177
            +E     +  I ATTE     +   +LSRC+ F L ++ +  ++ +  +          
Sbjct: 245 HVENGD--ITLIGATTENPSFQLNAALLSRCRVFVLEKLPVNAVVTILMRAIASLGDSER 302

Query: 178 ----LQEESIEFDPEAVAMIARASDGSARDGLSLLDQAIA 213
               L   S+  +   +  +A  SDG AR  L+ L+ +++
Sbjct: 303 PTDPLPNSSMFVEDSIIDYLAYLSDGDARAALNALEMSLS 342


>gnl|CDD|37246 KOG2035, KOG2035, KOG2035, Replication factor C, subunit RFC3
           [Energy production and conversion, Replication,
           recombination and repair].
          Length = 351

 Score = 46.5 bits (110), Expect = 1e-05
 Identities = 42/212 (19%), Positives = 99/212 (46%), Gaps = 12/212 (5%)

Query: 73  NHVDVVELDAASHTSIDDVREIIDQI-YYKPI----SARFRVYIMDEVQMLSTAAFNGLL 127
            H+++   DA ++  +  ++E++ ++   + I       F+V +++E   L+  A + L 
Sbjct: 90  YHLEITPSDAGNYDRVV-IQELLKEVAQTQQIETQGQRPFKVVVINEADELTRDAQHALR 148

Query: 128 KTLEEPPPHVKFIFATTEIRKIPITVLSRCQRFDLHRISIGDLIELFTKILQEESIEFDP 187
           +T+E+   + + I       +I   + SRC    +   S  ++  + +K+L++E ++   
Sbjct: 149 RTMEKYSSNCRLILVCNSTSRIIEPIRSRCLFIRVPAPSDEEITSVLSKVLKKEGLQLPK 208

Query: 188 EAVAMIARASDGSARDGLSLLDQAIARCNDKIVTSSVRLMLALADRNRIMDLFGYLIKGD 247
           E +  IA  S+ + R  L +L+    R N++  T++ +++        I ++   ++K  
Sbjct: 209 ELLKRIAEKSNRNLRRALLMLE--AVRVNNEPFTANSQVIPKPDWEIYIQEIARVILKEQ 266

Query: 248 IINVLQEFSSQ-YD---SGVNPSVILHDLAEF 275
               L E   + Y+     + P+ IL +L E 
Sbjct: 267 SPAKLLEVRGRLYELLSHCIPPNTILKELLEE 298


>gnl|CDD|35960 KOG0741, KOG0741, KOG0741, AAA+-type ATPase [Posttranslational
           modification, protein turnover, chaperones].
          Length = 744

 Score = 41.9 bits (98), Expect = 3e-04
 Identities = 47/222 (21%), Positives = 84/222 (37%), Gaps = 44/222 (19%)

Query: 23  SYMLSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFEGFGEHCQAIIRGNHVDVVELDA 82
           S +L G  G GKT  A  IA S ++    I  P  +  G  E  +      H+  +  DA
Sbjct: 540 SVLLEGPPGSGKTALAAKIALSSDFPFVKIISPE-DMIGLSESAKC----AHIKKIFEDA 594

Query: 83  ----ASHTSIDDVREIIDQIYYKPISARFRVYIMDEVQMLSTAAFNGLLKTLEEPPP--H 136
                S   +DD+  ++D   Y PI  RF           S      LL  L++ PP   
Sbjct: 595 YKSPLSIIVVDDIERLLD---YVPIGPRF-----------SNLVLQALLVLLKKQPPKGR 640

Query: 137 VKFIFATTEIRKIPITVLSRCQRFDLHRISIGDLIELFTKILQEESIEFDPEAVAMIARA 196
              IF TT  R     VL               +++ F+  +   ++    + + ++   
Sbjct: 641 KLLIFGTTSRR----EVLQEM-----------GILDCFSSTIHVPNLTTGEQLLEVLEEL 685

Query: 197 SDGSARDGLSLLDQAIARCNDKIVTSSVRLMLALADRNRIMD 238
           +  S  +  ++ +Q +++     V   ++ +L L +  R  +
Sbjct: 686 NIFSDDEVRAIAEQLLSKK----VNVGIKKLLMLIEMARQDE 723


>gnl|CDD|143797 pfam00004, AAA, ATPase family associated with various cellular
           activities (AAA).  AAA family proteins often perform
           chaperone-like functions that assist in the assembly,
           operation, or disassembly of protein complexes.
          Length = 131

 Score = 41.1 bits (97), Expect = 5e-04
 Identities = 29/143 (20%), Positives = 49/143 (34%), Gaps = 23/143 (16%)

Query: 24  YMLSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFEGFGEHCQAIIRGNHVDVVELDAA 83
            +L G  G GKTT A+ +A+ L      I    +  +  GE  + +           +AA
Sbjct: 1   LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLREL-------FEAA 53

Query: 84  SHTS-----IDDVREIIDQIYYKPISARFRVYIMDEVQMLSTAAFNGLLKTLEEPPPHVK 138
              +     ID+    ID +      +R      +  ++++       L         V 
Sbjct: 54  KKLAPCVIFIDE----IDAL----AGSRGSGGDSESRRVVN--QLLTELDGFTSSLSKVI 103

Query: 139 FIFATTEIRKIPITVL-SRCQRF 160
            I AT    K+   +L  R  R 
Sbjct: 104 VIAATNRPDKLDPALLRGRFDRI 126


>gnl|CDD|32436 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
           replication, recombination, and repair].
          Length = 332

 Score = 37.4 bits (87), Expect = 0.006
 Identities = 59/241 (24%), Positives = 95/241 (39%), Gaps = 31/241 (12%)

Query: 2   IGQKPMIKTLTNAFKSGRIAQS----YMLSGTRGIGKTTTARIIARSLNYKTAHIDVPTV 57
           IGQ+ + + L    K+ +         +L G  G+GKTT A IIA  L         P +
Sbjct: 29  IGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANELGVNLKITSGPAL 88

Query: 58  EFEGFGEHCQAIIRG-NHVDVVELDAASHTSIDDVREIIDQIYYKPISARFRVYIMDEVQ 116
           E  G      AI+      DV+ +D      I  +   ++++ Y P    FR+ I+  + 
Sbjct: 89  EKPG---DLAAILTNLEEGDVLFID-----EIHRLSPAVEEVLY-PAMEDFRLDII--IG 137

Query: 117 MLSTAAFNGLLKTLEEPPPHVKFIFATTEIRKIPITVLSR---CQRFDLHRISIGDLIEL 173
               A      +++    P    I ATT    +   +  R    QR + +  ++ +L E+
Sbjct: 138 KGPAA------RSIRLDLPPFTLIGATTRAGMLTNPLRDRFGIIQRLEFY--TVEELEEI 189

Query: 174 FTKILQEESIEFDPEAVAMIARASDGSARDGLSLL----DQAIARCNDKIVTSSVRLMLA 229
             +  +   IE D EA   IAR S G+ R    LL    D A  + +  I        L 
Sbjct: 190 VKRSAKILGIEIDEEAALEIARRSRGTPRIANRLLRRVRDFAQVKGDGDIDRDIADKALK 249

Query: 230 L 230
           +
Sbjct: 250 M 250


>gnl|CDD|35285 KOG0062, KOG0062, KOG0062, ATPase component of ABC transporters
           with duplicated ATPase domains/Translation elongation
           factor EF-3b [Amino acid transport and metabolism,
           Translation, ribosomal structure and biogenesis].
          Length = 582

 Score = 37.2 bits (86), Expect = 0.008
 Identities = 25/102 (24%), Positives = 39/102 (38%), Gaps = 9/102 (8%)

Query: 24  YMLSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFEGFGEHCQAIIRGNHVDVVELDAA 83
           Y L G  GIGK+T  R IA         +    VE E  G+  +A+      D   LD  
Sbjct: 109 YGLVGRNGIGKSTLLRAIAN------GQVSGFHVEQEVRGDDTEALQSVLESDTERLDFL 162

Query: 84  SHTSIDDVREIIDQIYYKPISARFRVYIMDEVQMLSTAAFNG 125
           +          +++IY         +    E+Q+  T + +G
Sbjct: 163 AEEKELLAGLTLEEIY---DKILAGLGFTPEMQLQPTKSLSG 201


>gnl|CDD|37180 KOG1969, KOG1969, KOG1969, DNA replication checkpoint protein
           CHL12/CTF18 [Energy production and conversion,
           Replication, recombination and repair].
          Length = 877

 Score = 35.8 bits (82), Expect = 0.018
 Identities = 12/29 (41%), Positives = 17/29 (58%)

Query: 25  MLSGTRGIGKTTTARIIARSLNYKTAHID 53
           +L G  G+GKTT A +IA+   Y    I+
Sbjct: 330 LLCGPPGLGKTTLAHVIAKQAGYSVVEIN 358


>gnl|CDD|37153 KOG1942, KOG1942, KOG1942, DNA helicase, TBP-interacting protein
           [Replication, recombination and repair].
          Length = 456

 Score = 34.2 bits (78), Expect = 0.066
 Identities = 35/146 (23%), Positives = 59/146 (40%), Gaps = 20/146 (13%)

Query: 109 VYIMDEVQMLSTAAFNGLLKTLEEPPPHVKFIFAT----TEIR---------KIPITVLS 155
           V  +DEV ML    F  L K LE P   +  IFA+      IR          IP  +L 
Sbjct: 299 VLFIDEVHMLDIECFTYLHKALESPIAPI-VIFASNRGMCTIRGTEDILSPHGIPPDLLD 357

Query: 156 RCQRFDLHRISIGDLIELFTKILQEESIEFDPEAVAMIAR-ASDGSARDGLSLLDQAIAR 214
           R            ++ ++     Q E ++ + EA+ ++A   +  S R  + LL  A   
Sbjct: 358 RLLIIRTLPYDEEEIRQIIKIRAQVEGLQVEEEALDLLAEIGTSTSLRYAVQLLTPA--- 414

Query: 215 CNDKIVTSSVRLMLALADRNRIMDLF 240
               +  ++ R  +++ D   + +LF
Sbjct: 415 --SILAKTNGRKEISVEDVEEVTELF 438


>gnl|CDD|73296 cd02020, CMPK, Cytidine monophosphate kinase (CMPK) catalyzes the
          reversible phosphorylation of cytidine monophosphate
          (CMP) to produce cytidine diphosphate (CDP), using ATP
          as the preferred phosphoryl donor..
          Length = 147

 Score = 33.2 bits (76), Expect = 0.11
 Identities = 16/73 (21%), Positives = 32/73 (43%), Gaps = 18/73 (24%)

Query: 26 LSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFEGFGEHCQAIIRGNHVDVVELDAASH 85
          + G  G GK+T A+++A+ L     ++D   +  E  G+                 A+  
Sbjct: 4  IDGPAGSGKSTVAKLLAKKLGLP--YLDTGGIRTEEVGKL----------------ASEV 45

Query: 86 TSIDDVREIIDQI 98
           +I +VR+ +D+ 
Sbjct: 46 AAIPEVRKALDER 58


>gnl|CDD|31663 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
           replication, recombination, and repair /
           Posttranslational modification, protein turnover,
           chaperones].
          Length = 366

 Score = 32.6 bits (74), Expect = 0.17
 Identities = 50/260 (19%), Positives = 86/260 (33%), Gaps = 30/260 (11%)

Query: 8   IKTLTNAFKS---GRIAQSYMLSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFEGFGE 64
           I  L +       G    + ++ G  G GKT T + +   L   +A+++V  +       
Sbjct: 26  INQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRT 85

Query: 65  HCQAIIR-GNHVDVVELDAASHTSIDDVREIIDQIYYKPISARFRVYI--MDEVQMLSTA 121
             Q + +  N +  V L   S          I +  Y  +S + +  I  +DEV  L   
Sbjct: 86  PYQVLSKILNKLGKVPLTGDSSLE-------ILKRLYDNLSKKGKTVIVILDEVDALVDK 138

Query: 122 AFNGLLKTLEEP-PPHVKF-IFATTEIRKIPITVLSR-CQRFDLHRISIGDLI--ELFTK 176
               L   L  P    VK  I A +   K    +  R         I        EL+  
Sbjct: 139 DGEVLYSLLRAPGENKVKVSIIAVSNDDKFLDYLDPRVKSSLGPSEIVFPPYTAEELYDI 198

Query: 177 ILQEESIEFDP--------EAVAMIARASDGSARDGLSLLD----QAIARCNDKIVTSSV 224
           + +     F          + +A +  A  G AR  + +L      A    + K+    V
Sbjct: 199 LRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHV 258

Query: 225 RLMLALADRNRIMDLFGYLI 244
           R      +R+ + ++   L 
Sbjct: 259 REAQEEIERDVLEEVLKTLP 278


>gnl|CDD|35955 KOG0736, KOG0736, KOG0736, Peroxisome assembly factor 2 containing
           the AAA+-type ATPase domain [Posttranslational
           modification, protein turnover, chaperones].
          Length = 953

 Score = 32.7 bits (74), Expect = 0.19
 Identities = 49/275 (17%), Positives = 90/275 (32%), Gaps = 46/275 (16%)

Query: 17  SGRIAQSYMLSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFEGFGEHCQAIIRGNHVD 76
              +  S +L G  G GKTT  R +A         + +  +E + +    ++        
Sbjct: 427 LLTLNPSVLLHGPPGSGKTTVVRAVAS-------ELGLHLLEVDCYELVAES-------- 471

Query: 77  VVELDAASHTSIDDVREIIDQIYYKPISARFRVYIMDEVQMLSTAAFNG----LLKTLEE 132
                 ASHT        +  I+ +       V  +  + +L      G    LLK +  
Sbjct: 472 ------ASHTETK-----LQAIFSRARRCSPAVLFLRNLDVLGIDQDGGEDARLLKVIRH 520

Query: 133 ---------PPPHVKFIFATTEIRKIPITVLSRCQRFDLH--RISIGDLIELFTKILQEE 181
                      P V  +  T+ I  +P  + S     ++    +S    +E+    L   
Sbjct: 521 LLSNEDFKFSCPPVIVVATTSSIEDLPADIQS-LFLHEIEVPALSEEQRLEILQWYLNHL 579

Query: 182 SIEFDPEAVAMIARASDGSARDGLSLLDQAIARCNDKIVTSSVRLMLALADRNRIMDLFG 241
            +  D     +  + S  S  D  +L+  +      +I    +   L   D   +     
Sbjct: 580 PLNQDVNLKQLARKTSGFSFGDLEALVAHSSLAAKTRIKNKGLAGGLQEEDEGELCAAGF 639

Query: 242 YLIKGDI---INVLQ-EFSSQYDSGVNPSVILHDL 272
            L + D    ++ LQ EFS    +   P+V   D+
Sbjct: 640 LLTEEDFDKALSRLQKEFSDAIGAPKIPNVSWDDV 674


>gnl|CDD|37891 KOG2680, KOG2680, KOG2680, DNA helicase TIP49, TBP-interacting
           protein [Transcription].
          Length = 454

 Score = 32.2 bits (73), Expect = 0.24
 Identities = 44/167 (26%), Positives = 67/167 (40%), Gaps = 27/167 (16%)

Query: 109 VYIMDEVQMLSTAAFNGLLKTLEEPPPHVKFIFAT----TEIR--------KIPITVLSR 156
           V  +DEV ML    F+ L + LE     +  I AT    T IR         IPI +L R
Sbjct: 291 VLFIDEVHMLDIECFSFLNRALENDMAPI-IIMATNRGITRIRGTNYRSPHGIPIDLLDR 349

Query: 157 CQRFDLHRISIGDLIELFTKILQEESIEFDPEAVAMIAR-ASDGSARDGLSLLDQAIARC 215
                    +  D+ ++     QEE +E +P+A+ ++ +     S R  + L+  A   C
Sbjct: 350 MLIISTQPYTEEDIKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVC 409

Query: 216 ---NDKIVTSSVRLMLALADRNRIMDLFGYLIKGDIINVLQEFSSQY 259
                K+V           D  R+  LF  L +   +  L E+ S Y
Sbjct: 410 LKRKGKVVEVD--------DIERVYRLF--LDEKRSMKYLTEYQSGY 446


>gnl|CDD|30793 COG0444, DppD, ABC-type dipeptide/oligopeptide/nickel transport
           system, ATPase component [Amino acid transport and
           metabolism / Inorganic ion transport and metabolism].
          Length = 316

 Score = 31.3 bits (71), Expect = 0.41
 Identities = 23/82 (28%), Positives = 34/82 (41%), Gaps = 7/82 (8%)

Query: 22  QSYMLSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFEG-----FGEHCQAIIRGNHVD 76
           +   + G  G GK+  A+ I   L    A I    + F+G       E     IRG  + 
Sbjct: 32  EILGIVGESGSGKSVLAKAIMGLLPKPNARIVGGEILFDGKDLLSLSEKELRKIRGKEIA 91

Query: 77  VVELDAASHTSIDDVREIIDQI 98
           ++  D    TS++ V  I DQI
Sbjct: 92  MIFQDPM--TSLNPVMTIGDQI 111


>gnl|CDD|147593 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB
          N-terminus.  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. Branch migration is
          catalysed by the RuvB protein that is targeted to the
          Holliday junction by the structure specific RuvA
          protein. This family contains the N-terminal region of
          the protein.
          Length = 234

 Score = 30.9 bits (71), Expect = 0.67
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 4/49 (8%)

Query: 2  IGQKPMIKTLTNAFKSGRIAQSYM----LSGTRGIGKTTTARIIARSLN 46
          IGQ+ + + L    ++ +     +    L G  G+GKTT A IIA  + 
Sbjct: 27 IGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMG 75


>gnl|CDD|30188 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the
          shikimate pathway, a seven-step biosynthetic pathway
          which converts erythrose-4-phosphate to chorismic acid,
          found in bacteria, fungi and plants. Chorismic acid is
          a important intermediate in the synthesis of aromatic
          compounds, such as aromatic amino acids, p-aminobenzoic
          acid, folate and ubiquinone. Shikimate kinase catalyses
          the phosphorylation of the 3-hydroxyl group of shikimic
          acid using ATP..
          Length = 154

 Score = 30.6 bits (69), Expect = 0.72
 Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 2/46 (4%)

Query: 26 LSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFEGFGEHCQAIIR 71
          L G  G GKTT  R++A++L      +D+  +  +  G     I  
Sbjct: 4  LIGMMGAGKTTVGRLLAKALGLP--FVDLDELIEQRAGMSIPEIFA 47


>gnl|CDD|32994 COG3181, COG3181, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 319

 Score = 30.3 bits (68), Expect = 0.80
 Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 4/57 (7%)

Query: 28  GTRGIGKTTTARIIARSLNYKTAHIDVPTVEFEGFGEHCQAIIRGNHVDVVELDAAS 84
           G  G+G   +A  +A +L  K A I +  V ++G GE   A++ G HVD    + + 
Sbjct: 154 GGSGLG---SADHLAGALFAKAAGIKITYVPYKGGGEALTALL-GGHVDAGSTNLSE 206


>gnl|CDD|37215 KOG2004, KOG2004, KOG2004, Mitochondrial ATP-dependent protease
           PIM1/LON [Posttranslational modification, protein
           turnover, chaperones].
          Length = 906

 Score = 30.3 bits (68), Expect = 0.84
 Identities = 12/23 (52%), Positives = 16/23 (69%)

Query: 26  LSGTRGIGKTTTARIIARSLNYK 48
             G  G+GKT+ A+ IAR+LN K
Sbjct: 443 FVGPPGVGKTSIAKSIARALNRK 465


>gnl|CDD|37179 KOG1968, KOG1968, KOG1968, Replication factor C, subunit RFC1
           (large subunit) [Replication, recombination and repair].
          Length = 871

 Score = 29.6 bits (66), Expect = 1.3
 Identities = 13/29 (44%), Positives = 17/29 (58%)

Query: 25  MLSGTRGIGKTTTARIIARSLNYKTAHID 53
           +LSG  GIGKTT A   A+ L +K    +
Sbjct: 361 LLSGPPGIGKTTAAHKAAKELGFKVVEKN 389


>gnl|CDD|144702 pfam01202, SKI, Shikimate kinase. 
          Length = 158

 Score = 29.9 bits (68), Expect = 1.3
 Identities = 8/19 (42%), Positives = 12/19 (63%)

Query: 30 RGIGKTTTARIIARSLNYK 48
           G GKTT  R++A++L   
Sbjct: 1  MGAGKTTIGRLLAKALGLP 19


>gnl|CDD|73336 cd02987, Phd_like_Phd, Phosducin (Phd)-like family, Phd subfamily;
           Phd is a cytosolic regulator of G protein functions. It
           specifically binds G protein betagamma (Gbg)-subunits
           with high affinity, resulting in the solubilization of
           Gbg from the plasma membrane. This impedes the formation
           of a functional G protein trimer (G protein
           alphabetagamma), thereby inhibiting G protein-mediated
           signal transduction. Phd also inhibits the GTPase
           activity of G protein alpha. Phd can be phosphorylated
           by protein kinase A and G protein-coupled receptor
           kinase 2, leading to its inactivation. Phd was
           originally isolated from the retina, where it is highly
           expressed and has been implicated to play an important
           role in light adaptation. It is also found in the pineal
           gland, liver, spleen, striated muscle and the brain. The
           C-terminal domain of Phd adopts a thioredoxin fold, but
           it does not contain a CXXC motif. Phd interacts with G
           protein beta mostly through the N-terminal helical
           domain..
          Length = 175

 Score = 29.4 bits (66), Expect = 1.4
 Identities = 25/110 (22%), Positives = 41/110 (37%), Gaps = 14/110 (12%)

Query: 87  SIDDVREIIDQIYYKPISARFRVYIMDEVQMLSTAAFNGLLKTLEEPPPHVKFIFATTEI 146
            +D   + +D I  +       V+I +   +   AA N  L  L    P VKF       
Sbjct: 66  ELDSGEQFLDAIDKEGKDTTVVVHIYEP-GIPGCAALNSSLLCLAAEYPAVKFC------ 118

Query: 147 RKIPITVLSRCQRFDLHRI------SIGDLIELFTKILQEESIEFDPEAV 190
            KI  +       FD   +        G+LI  F ++ ++   +FD E +
Sbjct: 119 -KIRASATGASDEFDTDALPALLVYKGGELIGNFVRVTEDLGEDFDAEDL 167


>gnl|CDD|31047 COG0703, AroK, Shikimate kinase [Amino acid transport and
          metabolism].
          Length = 172

 Score = 29.4 bits (66), Expect = 1.8
 Identities = 11/33 (33%), Positives = 17/33 (51%)

Query: 21 AQSYMLSGTRGIGKTTTARIIARSLNYKTAHID 53
            + +L G  G GK+T  R +A++LN      D
Sbjct: 2  NMNIVLIGFMGAGKSTIGRALAKALNLPFIDTD 34


>gnl|CDD|31417 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
           [Transcription].
          Length = 450

 Score = 29.1 bits (65), Expect = 2.0
 Identities = 32/116 (27%), Positives = 48/116 (41%), Gaps = 14/116 (12%)

Query: 109 VYIMDEVQMLSTAAFNGLLKTLEEPPPHVKFIFAT----TEIR--------KIPITVLSR 156
           V  +DEV ML    F+ L + LE     +  I AT    T+IR         IP+ +L R
Sbjct: 294 VLFIDEVHMLDIECFSFLNRALESELAPI-IILATNRGMTKIRGTDIESPHGIPLDLLDR 352

Query: 157 CQRFDLHRISIGDLIELFTKILQEESIEFDPEAVAMIAR-ASDGSARDGLSLLDQA 211
                    S  ++ E+     +EE IE   +A+  +     + S R  + LL  A
Sbjct: 353 LLIISTRPYSREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPA 408


>gnl|CDD|37135 KOG1924, KOG1924, KOG1924, RhoA GTPase effector DIA/Diaphanous
           [Signal transduction mechanisms, Cytoskeleton].
          Length = 1102

 Score = 29.2 bits (65), Expect = 2.1
 Identities = 17/90 (18%), Positives = 34/90 (37%), Gaps = 21/90 (23%)

Query: 199 GSARDGLSLLDQAIARCNDKIVTSSVRLMLALADRNRIMDLFGYLIKGDIINVLQEFSSQ 258
           GS R     +   I   N+ +++ S+           I +L  +L + + +N L E  ++
Sbjct: 709 GSFRMPYEEIKNVILEVNEDVLSESM-----------IQNLIKHLPEQEQLNKLSELKAE 757

Query: 259 YDSGVNPSVILHDLAEFTHLVTRIKYIPEM 288
           Y+          DL E    V  +  +  +
Sbjct: 758 YE----------DLPEPEQFVVVMSQVKRL 777


>gnl|CDD|31270 COG1072, CoaA, Panthothenate kinase [Coenzyme metabolism].
          Length = 283

 Score = 29.1 bits (65), Expect = 2.2
 Identities = 13/37 (35%), Positives = 21/37 (56%)

Query: 26  LSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFEGF 62
           ++G+  +GK+TTARI+   L+       V  V  +GF
Sbjct: 87  IAGSVAVGKSTTARILQALLSRWPESPKVDLVTMDGF 123


>gnl|CDD|30198 cd02025, PanK, Pantothenate kinase (PanK) catalyzes the
          phosphorylation of pantothenic acid to form
          4'-phosphopantothenic, which is the first of five steps
          in coenzyme A (CoA) biosynthetic pathway. The reaction
          carried out by this enzyme is a key regulatory point in
          CoA biosynthesis..
          Length = 220

 Score = 28.7 bits (64), Expect = 2.4
 Identities = 12/37 (32%), Positives = 23/37 (62%)

Query: 26 LSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFEGF 62
          ++G+  +GK+TTAR++   L+    H +V  +  +GF
Sbjct: 4  IAGSVAVGKSTTARVLQALLSRWPDHPNVELITTDGF 40


>gnl|CDD|33889 COG4133, CcmA, ABC-type transport system involved in cytochrome c
          biogenesis, ATPase component [Posttranslational
          modification, protein turnover, chaperones].
          Length = 209

 Score = 28.7 bits (64), Expect = 2.9
 Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 3/40 (7%)

Query: 3  GQKPMIKTLTNAFKSGRIAQSYMLSGTRGIGKTTTARIIA 42
          G++ +   L+    +G   Q   ++G  G GKTT  RI+A
Sbjct: 13 GERTLFSDLSFTLNAGEALQ---ITGPNGAGKTTLLRILA 49


>gnl|CDD|31058 COG0714, COG0714, MoxR-like ATPases [General function prediction
          only].
          Length = 329

 Score = 28.5 bits (63), Expect = 3.1
 Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 3/52 (5%)

Query: 1  MIGQKPMIKTLTNAFKSGRIAQSYMLSGTRGIGKTTTARIIARSLNYKTAHI 52
          ++G + +I+    A  +G      +L G  G+GKT  AR +AR+L      I
Sbjct: 26 VVGDEEVIELALLALLAGGHV---LLEGPPGVGKTLLARALARALGLPFVRI 74


>gnl|CDD|30106 cd01384, MYSc_type_XI, Myosin motor domain, plant-specific type XI
           myosin, involved in organelle transport. This catalytic
           (head) domain has ATPase activity and belongs to the
           larger group of P-loop NTPases. Myosins are
           actin-dependent molecular motors that play important
           roles in muscle contraction, cell motility, and
           organelle transport. The head domain is a molecular
           motor, which utilizes ATP hydrolysis to generate
           directed movement toward the plus end along actin
           filaments. A cyclical interaction between myosin and
           actin provides the driving force. Rates of ATP
           hydrolysis and consequently the speed of movement along
           actin filaments vary widely, from about 0.04 micrometer
           per second for myosin I to 4.5 micrometer per second for
           myosin II in skeletal muscle. Myosin II moves in
           discrete steps about 5-10 nm long and generates 1-5
           piconewtons of force. Upon ATP binding, the myosin head
           dissociates from an actin filament. ATP hydrolysis
           causes the head to pivot and associate with a new actin
           subunit. The release of Pi causes the head to pivot and
           move the filament (power stroke). Release of ADP
           completes the cycle..
          Length = 674

 Score = 28.3 bits (63), Expect = 3.3
 Identities = 13/35 (37%), Positives = 19/35 (54%)

Query: 20  IAQSYMLSGTRGIGKTTTARIIARSLNYKTAHIDV 54
            +QS ++SG  G GKT T +++ R L Y      V
Sbjct: 87  KSQSILVSGESGAGKTETTKMLMRYLAYMGGRAGV 121


>gnl|CDD|35911 KOG0692, KOG0692, KOG0692, Pentafunctional AROM protein [Amino acid
           transport and metabolism].
          Length = 595

 Score = 28.4 bits (63), Expect = 3.3
 Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 10  TLTNAFKSGRIAQSYM-LSGTRGIGKTTTARIIARSLNYKTAHID 53
           T     +SG I  S M + G R  GKTT  +  A+ L +K   +D
Sbjct: 551 TGAEPLESGAIKNSSMFVIGMREAGKTTIGKPAAKELYWKIMDLD 595


>gnl|CDD|145705 pfam02689, Herpes_Helicase, Helicase.  This family consists of
           Helicases from the Herpes viruses. Helicases are
           responsible for the unwinding of DNA and are essential
           for replication and completion of the viral life cycle.
          Length = 801

 Score = 28.4 bits (64), Expect = 3.4
 Identities = 30/135 (22%), Positives = 56/135 (41%), Gaps = 39/135 (28%)

Query: 23  SYMLSGTRGIGKTTTARIIARSLN--------------------YKTAHIDVPTVEFEGF 62
           +Y+++GT G GK+T+ + +  +L+                      +A+   PT+ F+ F
Sbjct: 62  AYLITGTAGAGKSTSIQTLNENLDCLITGATRVAAQNLSAKLSRAYSAYC--PTI-FQAF 118

Query: 63  GEHCQAIIRGNHVDVVE----LDAASHTSIDDVREIIDQIYYKP----ISARF-RVYIMD 113
           G       + NHV+       +   +  SI+++ +  D +YY P    I  RF +   + 
Sbjct: 119 G------FKSNHVNAQLRYSYVPPTTPPSIEEL-QKRDLVYYWPVIADIIRRFLKKKRLG 171

Query: 114 EVQMLSTAAFNGLLK 128
           +    S  A   L K
Sbjct: 172 QYASGSLEALAPLCK 186


>gnl|CDD|37181 KOG1970, KOG1970, KOG1970, Checkpoint RAD17-RFC complex,
           RAD17/RAD24 component [Energy production and conversion,
           Replication, recombination and repair].
          Length = 634

 Score = 28.1 bits (62), Expect = 3.5
 Identities = 9/24 (37%), Positives = 18/24 (75%)

Query: 25  MLSGTRGIGKTTTARIIARSLNYK 48
           +L+G  G GK+TT +++++ L Y+
Sbjct: 114 LLTGPSGCGKSTTVKVLSKELGYQ 137


>gnl|CDD|177020 CHL00081, chlI, Mg-protoporyphyrin IX chelatase.
          Length = 350

 Score = 28.4 bits (64), Expect = 3.6
 Identities = 9/18 (50%), Positives = 12/18 (66%)

Query: 25 MLSGTRGIGKTTTARIIA 42
          M+ G RG GK+TT R + 
Sbjct: 42 MIMGDRGTGKSTTIRALV 59


>gnl|CDD|38557 KOG3347, KOG3347, KOG3347, Predicted nucleotide kinase/nuclear
          protein involved oxidative stress response [Nucleotide
          transport and metabolism].
          Length = 176

 Score = 28.3 bits (63), Expect = 4.0
 Identities = 9/30 (30%), Positives = 18/30 (60%), Gaps = 2/30 (6%)

Query: 25 MLSGTRGIGKTTTARIIARSLNYKTAHIDV 54
          +++GT G GK+T A  +A     +  +I++
Sbjct: 11 LVTGTPGTGKSTLAERLAEKTGLE--YIEI 38


>gnl|CDD|31317 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
          systems, ATPase components [Inorganic ion transport and
          metabolism / Coenzyme metabolism].
          Length = 258

 Score = 28.2 bits (63), Expect = 4.1
 Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 3/50 (6%)

Query: 3  GQKPMIKTLTNAFKSGRIAQSYMLSGTRGIGKTTTARIIARSLNYKTAHI 52
          G KP++  L+ +   G I     + G  G GK+T  + +A  L  K+  +
Sbjct: 13 GGKPILDDLSFSIPKGEIT---GILGPNGSGKSTLLKCLAGLLKPKSGEV 59


>gnl|CDD|30853 COG0507, RecD, ATP-dependent exoDNAse (exonuclease V), alpha
           subunit - helicase superfamily I member [DNA
           replication, recombination, and repair].
          Length = 696

 Score = 28.2 bits (62), Expect = 4.1
 Identities = 43/193 (22%), Positives = 65/193 (33%), Gaps = 36/193 (18%)

Query: 25  MLSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFEGFGEHCQAIIRGNHV-DVVELDAA 83
           ML+G  G GKTT  + IAR +              EG G+   A   G     + E    
Sbjct: 338 MLTGGPGTGKTTAIKAIARLI-------------KEGDGDQLLAAPTGKAAKRLNESTGL 384

Query: 84  SHTSIDDVREIIDQIYYKPISARFRVYIMDEVQMLSTAAFNGLLKTL------------E 131
              +I  +  + ++           + I+DE  ML T+   GLL  +            +
Sbjct: 385 EARTIHRLLGLWEKTGNNEEPLDGDLLIIDEASMLDTSLAFGLLSAIGKLAKVILVGDVD 444

Query: 132 EPPPHV--KFIFATTEIRKIPITVLSRCQR--------FDLHRISIGDLIELFTKILQEE 181
           + P            E   IP   L +  R            +I  G L  L T  +Q+ 
Sbjct: 445 QLPSVGAGAVFRDLIESIGIPELKLEKRFRQARDSSIILAAGQIYEGLLPLLATGRIQDR 504

Query: 182 SIEFDPEAVAMIA 194
           S E   + VA + 
Sbjct: 505 SAEAADQLVAAVE 517


>gnl|CDD|146043 pfam03215, Rad17, Rad17 cell cycle checkpoint protein. 
          Length = 490

 Score = 28.1 bits (62), Expect = 4.5
 Identities = 10/38 (26%), Positives = 19/38 (50%)

Query: 11 LTNAFKSGRIAQSYMLSGTRGIGKTTTARIIARSLNYK 48
          L   F         +L+G  G GK+TT +++++ L  +
Sbjct: 35 LKAVFLESNKQLILLLTGPSGCGKSTTVKVLSKELGIE 72


>gnl|CDD|33903 COG4152, COG4152, ABC-type uncharacterized transport system,
          ATPase component [General function prediction only].
          Length = 300

 Score = 27.9 bits (62), Expect = 4.5
 Identities = 16/52 (30%), Positives = 21/52 (40%), Gaps = 3/52 (5%)

Query: 3  GQKPMIKTLTNAFKSGRIAQSYMLSGTRGIGKTTTARIIARSLNYKTAHIDV 54
          G K  +  ++     G I   + L G  G GKTTT R+I   L      I  
Sbjct: 13 GDKKAVDNISFEVPPGEI---FGLLGPNGAGKTTTFRMILGLLEPTEGEITW 61


>gnl|CDD|73295 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. 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..
          Length = 69

 Score = 28.0 bits (62), Expect = 4.6
 Identities = 11/37 (29%), Positives = 19/37 (51%)

Query: 26 LSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFEGF 62
          ++G  G GK+T A+ +A  L  ++  +    V  EG 
Sbjct: 4  ITGGSGSGKSTVAKKLAEQLGGRSVVVLDEIVILEGL 40


>gnl|CDD|39857 KOG4658, KOG4658, KOG4658, Apoptotic ATPase [Signal transduction
           mechanisms].
          Length = 889

 Score = 28.0 bits (62), Expect = 4.6
 Identities = 11/29 (37%), Positives = 14/29 (48%)

Query: 26  LSGTRGIGKTTTARIIARSLNYKTAHIDV 54
           + G  G+GKTT AR I    +    H D 
Sbjct: 184 IYGMGGVGKTTLARQIFNKFDEVGNHFDG 212


>gnl|CDD|32119 COG1936, COG1936, Predicted nucleotide kinase (related to CMP and
          AMP kinases) [Nucleotide transport and metabolism].
          Length = 180

 Score = 27.9 bits (62), Expect = 4.6
 Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 8/77 (10%)

Query: 26 LSGTRGIGKTTTARIIARSLNYKTAHIDVPTVE---FEGFGEHCQAIIRGNHVDVVELDA 82
          ++GT G+GKTT  +++   L YK   ++    E   +  + E  +++I    VDV +L  
Sbjct: 5  ITGTPGVGKTTVCKLLRE-LGYKVIELNELAKENGLYTEYDELRKSVI----VDVDKLRK 59

Query: 83 ASHTSIDDVREIIDQIY 99
               + +   I+D   
Sbjct: 60 RLEELLREGSGIVDSHL 76


>gnl|CDD|31432 COG1239, ChlI, Mg-chelatase subunit ChlI [Coenzyme metabolism].
          Length = 423

 Score = 28.0 bits (62), Expect = 4.8
 Identities = 10/31 (32%), Positives = 16/31 (51%)

Query: 25 MLSGTRGIGKTTTARIIARSLNYKTAHIDVP 55
          +++G +G  K+T AR +A  L      I  P
Sbjct: 42 LIAGEKGTAKSTLARALADLLPEIEVVIGCP 72


>gnl|CDD|35382 KOG0160, KOG0160, KOG0160, Myosin class V heavy chain
           [Cytoskeleton].
          Length = 862

 Score = 28.0 bits (62), Expect = 4.8
 Identities = 22/99 (22%), Positives = 41/99 (41%), Gaps = 17/99 (17%)

Query: 22  QSYMLSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFEGFGEHCQAIIRGNHVDVVELD 81
           QS ++SG  G GKT TA+ +   L      ++  ++E          ++  N +   E  
Sbjct: 95  QSIIVSGESGAGKTETAKYLMEYLASVGGSVEGRSIE--------NKVLASNPIL--EAF 144

Query: 82  AASHTSIDD-------VREIIDQIYYKPISARFRVYIMD 113
             + T+ +D       V EI      +   A+ R Y+++
Sbjct: 145 GNAKTTRNDNSSRFGKVIEITFDQQGRISGAKIRTYLLE 183


>gnl|CDD|31145 COG0802, COG0802, Predicted ATPase or kinase [General function
          prediction only].
          Length = 149

 Score = 27.5 bits (61), Expect = 5.8
 Identities = 21/71 (29%), Positives = 29/71 (40%), Gaps = 3/71 (4%)

Query: 26 LSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFEGFGEHCQAIIRGNHVDVVELDAASH 85
          LSG  G GKTT  R IA+ L     ++  PT  F    E+ +  +   H D+  L     
Sbjct: 30 LSGDLGAGKTTLVRGIAKGLGVDG-NVKSPT--FTLVEEYEEGRLPLYHFDLYRLSDPEE 86

Query: 86 TSIDDVREIID 96
               + E  D
Sbjct: 87 LDELGLDEYFD 97


>gnl|CDD|72989 cd03230, ABC_DR_subfamily_A, This family of ATP-binding proteins
          belongs to a multisubunit transporter involved in drug
          resistance (BcrA and DrrA), nodulation, lipid
          transport, and lantibiotic immunity.  In bacteria and
          archaea, these transporters usually include an
          ATP-binding protein and one or two integral membrane
          proteins.  Eukaryote systems of the ABCA subfamily
          display ABC domains that are quite similar to this
          family.  The ATP-binding domain shows the highest
          similarity between all members of the ABC transporter
          family.  ABC transporters are a subset of nucleotide
          hydrolases that contain a signature motif, Q-loop, and
          H-loop/switch region, in addition to, the Walker A
          motif/P-loop and Walker B motif commonly found in a
          number of ATP- and GTP-binding and hydrolyzing
          proteins..
          Length = 173

 Score = 27.7 bits (62), Expect = 5.8
 Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 3/40 (7%)

Query: 3  GQKPMIKTLTNAFKSGRIAQSYMLSGTRGIGKTTTARIIA 42
          G+K  +  ++   + G I   Y L G  G GKTT  +II 
Sbjct: 11 GKKTALDDISLTVEKGEI---YGLLGPNGAGKTTLIKIIL 47


>gnl|CDD|38232 KOG3022, KOG3022, KOG3022, Predicted ATPase, nucleotide-binding
          [Cell cycle control, cell division, chromosome
          partitioning].
          Length = 300

 Score = 27.6 bits (61), Expect = 6.1
 Identities = 11/32 (34%), Positives = 16/32 (50%), Gaps = 3/32 (9%)

Query: 26 LSGTRGIGKTTTARIIARSL---NYKTAHIDV 54
          LSG  G+GK+T    +A +L     K   +D 
Sbjct: 53 LSGKGGVGKSTVTVNLALALASEGKKVGLLDA 84


>gnl|CDD|146298 pfam03585, Herpes_ICP4_C, Herpesvirus ICP4-like protein C-terminal
           region.  The immediate-early protein ICP4 (infected-cell
           polypeptide 4) is required for efficient transcription
           of early and late viral genes and is thus essential for
           productive infection. ICP4 is a large phosphoprotein
           that binds DNA in a sequence specific manner as a
           homodimer. ICP4 represses transcription from LAT, ICP4
           and ORF-P that have high-affinity a ICP4 binding site
           that spans the transcription initiation site. ICP4
           proteins have two highly conserved regions, this family
           contains the C-terminal region that probably acts as an
           enhancer for the N-terminal region.
          Length = 425

 Score = 27.4 bits (61), Expect = 6.2
 Identities = 10/25 (40%), Positives = 14/25 (56%), Gaps = 1/25 (4%)

Query: 181 ESIEFDPEAVAMIA-RASDGSARDG 204
            ++ FDPEA+A IA R +    R  
Sbjct: 45  PALAFDPEALAEIAARCNGPPPRSD 69


>gnl|CDD|30814 COG0466, Lon, ATP-dependent Lon protease, bacterial type
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 782

 Score = 27.4 bits (61), Expect = 6.2
 Identities = 10/23 (43%), Positives = 15/23 (65%)

Query: 26  LSGTRGIGKTTTARIIARSLNYK 48
           L G  G+GKT+  + IA++L  K
Sbjct: 355 LVGPPGVGKTSLGKSIAKALGRK 377


>gnl|CDD|35286 KOG0063, KOG0063, KOG0063, RNAse L inhibitor, ABC superfamily [RNA
           processing and modification].
          Length = 592

 Score = 27.2 bits (60), Expect = 6.8
 Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 5/36 (13%)

Query: 12  TNAFKSGRI-----AQSYMLSGTRGIGKTTTARIIA 42
            N+FK  R+      Q   L GT GIGK+T  +I+A
Sbjct: 86  ANSFKLHRLPIPRPGQVLGLVGTNGIGKSTALKILA 121


>gnl|CDD|73054 cd03295, ABC_OpuCA_Osmoprotection, OpuCA is a the ATP binding
          component of a bacterial solute transporter that serves
          a protective role to cells growing in a hyperosmolar
          environment.  ABC (ATP-binding cassette) transporter
          nucleotide-binding domain; ABC transporters are a large
          family of proteins involved in the transport of a wide
          variety of different compounds, like sugars, ions,
          peptides, and more complex organic molecules.  The
          nucleotide binding domain shows the highest similarity
          between all members of the family.  ABC transporters
          are a subset of nucleotide hydrolases that contain a
          signature motif, Q-loop, and H-loop/switch region, in
          addition, to the Walker A motif/P-loop and Walker B
          motif commonly found in a number of ATP- and
          GTP-binding and hydrolyzing proteins..
          Length = 242

 Score = 27.5 bits (61), Expect = 6.8
 Identities = 14/41 (34%), Positives = 18/41 (43%), Gaps = 3/41 (7%)

Query: 3  GQKPMIKTLTNAFKSGRIAQSYMLSGTRGIGKTTTARIIAR 43
          G K  +  L      G      +L G  G GKTTT ++I R
Sbjct: 12 GGKKAVNNLNLEIAKGEFL---VLIGPSGSGKTTTMKMINR 49


>gnl|CDD|30084 cd00124, MYSc, Myosin motor domain. This catalytic (head) domain
           has ATPase activity and belongs to the larger group of
           P-loop NTPases. Myosins are actin-dependent molecular
           motors that play important roles in muscle contraction,
           cell motility, and organelle transport. The head domain
           is a molecular motor, which utilizes ATP hydrolysis to
           generate directed movement toward the plus end along
           actin filaments. A cyclical interaction between myosin
           and actin provides the driving force. Rates of ATP
           hydrolysis and consequently the speed of movement along
           actin filaments vary widely, from about 0.04 micrometer
           per second for myosin I to 4.5 micrometer per second for
           myosin II in skeletal muscle. Myosin II moves in
           discrete steps about 5-10 nm long and generates 1-5
           piconewtons of force. Upon ATP binding, the myosin head
           dissociates from an actin filament. ATP hydrolysis
           causes the head to pivot and associate with a new actin
           subunit. The release of Pi causes the head to pivot and
           move the filament (power stroke). Release of ADP
           completes the cycle..
          Length = 679

 Score = 27.2 bits (60), Expect = 6.9
 Identities = 12/37 (32%), Positives = 17/37 (45%)

Query: 22  QSYMLSGTRGIGKTTTARIIARSLNYKTAHIDVPTVE 58
           QS ++SG  G GKT   ++I + L       D    E
Sbjct: 87  QSIIISGESGAGKTENTKLIMKYLASLAGSNDTGIEE 123


>gnl|CDD|31326 COG1131, CcmA, ABC-type multidrug transport system, ATPase
          component [Defense mechanisms].
          Length = 293

 Score = 27.2 bits (60), Expect = 7.0
 Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 3/40 (7%)

Query: 3  GQKPMIKTLTNAFKSGRIAQSYMLSGTRGIGKTTTARIIA 42
          G K  +  ++   + G I   + L G  G GKTT  +I+A
Sbjct: 16 GDKTALDGVSFEVEPGEI---FGLLGPNGAGKTTLLKILA 52


>gnl|CDD|144489 pfam00910, RNA_helicase, RNA helicase.  This family includes RNA
          helicases thought to be involved in duplex unwinding
          during viral RNA replication. Members of this family
          are found in a variety of single stranded RNA viruses.
          Length = 105

 Score = 27.2 bits (61), Expect = 7.3
 Identities = 11/33 (33%), Positives = 16/33 (48%)

Query: 25 MLSGTRGIGKTTTARIIARSLNYKTAHIDVPTV 57
           L G  G GK+T A+ +AR+L          +V
Sbjct: 2  WLYGPPGCGKSTLAKYLARALLDHLGLPKKDSV 34



 Score = 26.8 bits (60), Expect = 8.7
 Identities = 19/68 (27%), Positives = 24/68 (35%), Gaps = 12/68 (17%)

Query: 234 NRIMDLFGYLIKGDI--INVLQEFSSQY---------DSGVNPSVILHDLAEFTHLVTRI 282
             ++D  G   K  +   N   +F   Y         D G NP     D AE   LV+  
Sbjct: 20  RALLDHLGLPKKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDG-PSDEAELIRLVSST 78

Query: 283 KYIPEMAD 290
            Y P MA 
Sbjct: 79  PYPPPMAA 86


>gnl|CDD|164554 CHL00175, minD, septum-site determining protein; Validated.
          Length = 281

 Score = 27.0 bits (60), Expect = 7.6
 Identities = 17/31 (54%), Positives = 20/31 (64%), Gaps = 5/31 (16%)

Query: 27 SGTRGIGKTT-TARI---IARSLNYKTAHID 53
          SG  G+GKTT TA +   IAR L Y+ A ID
Sbjct: 22 SGKGGVGKTTTTANLGMSIAR-LGYRVALID 51


>gnl|CDD|30812 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
           modification, protein turnover, chaperones].
          Length = 494

 Score = 27.1 bits (59), Expect = 7.6
 Identities = 34/180 (18%), Positives = 61/180 (33%), Gaps = 19/180 (10%)

Query: 25  MLSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFEGFGEHCQAIIRGNHVDVVELDAAS 84
           +L G  G GKT  A+ +A     +   +    +  +  GE  + I      +     A S
Sbjct: 280 LLYGPPGTGKTLLAKAVALESRSRFISVKGSELLSKWVGESEKNIRELF--EKARKLAPS 337

Query: 85  HTSIDDVREIIDQIYYKPISARFRVYIMDEVQMLSTAAFNGLLKTLEEPPPHVKFIFATT 144
              ID++  +          +  RV     V  L T   +G+ K           + A T
Sbjct: 338 IIFIDEIDSLASGRGPSEDGSGRRV-----VGQLLT-ELDGIEKA------EGVLVIAAT 385

Query: 145 EIRKIPITVLSRCQRFDLHRI----SIGDLIELFTKILQEESIEFDPEAV-AMIARASDG 199
                    L R  RFD         + + +E+F   L+++      +     +A  ++G
Sbjct: 386 NRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEG 445


>gnl|CDD|31320 COG1123, COG1123, ATPase components of various ABC-type transport
           systems, contain duplicated ATPase [General function
           prediction only].
          Length = 539

 Score = 27.1 bits (60), Expect = 9.1
 Identities = 10/18 (55%), Positives = 12/18 (66%)

Query: 26  LSGTRGIGKTTTARIIAR 43
           L G  G GK+T ARI+A 
Sbjct: 322 LVGESGSGKSTLARILAG 339


>gnl|CDD|31299 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
          metabolism].
          Length = 179

 Score = 26.7 bits (59), Expect = 9.3
 Identities = 12/23 (52%), Positives = 14/23 (60%)

Query: 26 LSGTRGIGKTTTARIIARSLNYK 48
          +SG  G GKTT AR +A  L  K
Sbjct: 5  ISGLPGSGKTTVARELAEHLGLK 27


>gnl|CDD|109737 pfam00693, Herpes_TK, Thymidine kinase from herpesvirus. 
          Length = 279

 Score = 26.9 bits (60), Expect = 9.8
 Identities = 11/16 (68%), Positives = 12/16 (75%)

Query: 28 GTRGIGKTTTARIIAR 43
          G  GIGKTTTAR +A 
Sbjct: 1  GAHGIGKTTTARALAA 16


>gnl|CDD|30834 COG0488, Uup, ATPase components of ABC transporters with duplicated
           ATPase domains [General function prediction only].
          Length = 530

 Score = 26.8 bits (59), Expect = 9.9
 Identities = 17/98 (17%), Positives = 37/98 (37%), Gaps = 5/98 (5%)

Query: 2   IGQKPMIKTLTNAFKSGRIAQSYMLSGTRGIGKTTTARIIARSLNYKTAHIDVPTVEFEG 61
            G +P+++ ++     G       L G  G GK+T  +I+A  L   +  +  P     G
Sbjct: 13  YGDRPLLENVSLTLNPGER---IGLVGRNGAGKSTLLKILAGELEPDSGEVTRPKGLRVG 69

Query: 62  FGEHCQAIIRGNHVDVVELDAASHTSIDDVREIIDQIY 99
           +    Q         V++        + ++   +++ Y
Sbjct: 70  YLS--QEPPLDPEKTVLDYVIEGFGELRELLAELEEAY 105


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.322    0.137    0.381 

Gapped
Lambda     K      H
   0.267   0.0868    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,357,737
Number of extensions: 234322
Number of successful extensions: 922
Number of sequences better than 10.0: 1
Number of HSP's gapped: 907
Number of HSP's successfully gapped: 111
Length of query: 369
Length of database: 6,263,737
Length adjustment: 95
Effective length of query: 274
Effective length of database: 4,210,882
Effective search space: 1153781668
Effective search space used: 1153781668
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 58 (25.9 bits)