RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|255764460|ref|YP_003064605.2| recombinase A [Candidatus
Liberibacter asiaticus str. psy62]
         (363 letters)



>gnl|CDD|143922 pfam00154, RecA, recA bacterial DNA recombination protein.  RecA is
           a DNA-dependent ATPase and functions in DNA repair
           systems. RecA protein catalyses an ATP-dependent DNA
           strand-exchange reaction that is the central step in the
           repair of dsDNA breaks by homologous recombination.
          Length = 322

 Score =  594 bits (1533), Expect = e-170
 Identities = 236/324 (72%), Positives = 284/324 (87%), Gaps = 2/324 (0%)

Query: 14  KALEAALSQIQRVYGKGAIMQLGSQGSIFEGIEVVSSGSLGLDIALGIGGFPKGRIVEIY 73
           KALEAALSQI++ +GKG+IM+LG +    E +EV+S+GSLGLDIALGIGG PKGRI+EIY
Sbjct: 1   KALEAALSQIEKQFGKGSIMRLGDKTV--EDVEVISTGSLGLDIALGIGGLPKGRIIEIY 58

Query: 74  GPESSGKTTLALHTIAQSQKTGGTCAFVDAEHALDSIYARKLGVDLKNLLISQPDTGEQA 133
           GPESSGKTTLALH IA++QK GGT AF+DAEHALD +YA+KLGVD+ NLL+SQPDTGEQA
Sbjct: 59  GPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQPDTGEQA 118

Query: 134 LEITDMLVRSGAVDIIVIDSVAALTPRAEIEGDMGESLPGMQARLMSQALRKLTSSISRS 193
           LEI DMLVRSGAVD+IV+DSVAAL P+AEIEG+MG+S  G+QARLMSQALRKLT +IS+S
Sbjct: 119 LEIADMLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGNISKS 178

Query: 194 KCILVFINQMRMKIGVMFGSPETTTGGNALKFYSSVRLDIRRVGSIKDKDSITGNQTRVK 253
              ++FINQ+RMKIGVMFG+PETTTGGNALKFY+SVRLDIRR+G+IK  + + GN+T+VK
Sbjct: 179 NTTVIFINQIRMKIGVMFGNPETTTGGNALKFYASVRLDIRRIGAIKKGEEVIGNRTKVK 238

Query: 254 VVKNKMASPFKQVEFDIMYGEGISFFGELIDLGVKASIVDKSGAWFSFKGQRLGQGRENS 313
           VVKNK+A PFKQ EFDIMYGEGIS  GELIDLGVK  IV+KSGAW+S+ G+++GQGREN+
Sbjct: 239 VVKNKVAPPFKQAEFDIMYGEGISKEGELIDLGVKLGIVEKSGAWYSYNGEKIGQGRENA 298

Query: 314 KIFLRENIEIAENIESLLRQNAGL 337
           K +L+EN EIA  IE  +R+  GL
Sbjct: 299 KQYLKENPEIAAEIEQKIREKLGL 322


>gnl|CDD|29984 cd00983, recA, RecA is a  bacterial enzyme which has roles in
           homologous recombination, DNA repair, and the induction
           of the SOS response.  RecA couples ATP hydrolysis to DNA
           strand exchange..
          Length = 325

 Score =  516 bits (1330), Expect = e-147
 Identities = 225/327 (68%), Positives = 277/327 (84%), Gaps = 2/327 (0%)

Query: 11  DKSKALEAALSQIQRVYGKGAIMQLGSQGSIFEGIEVVSSGSLGLDIALGIGGFPKGRIV 70
           +K KALE AL QI++ +GKG+IM+LG      + +EV+ +GSL LDIALGIGG+PKGRI+
Sbjct: 1   EKQKALELALKQIEKKFGKGSIMKLGDDAV--QDVEVIPTGSLSLDIALGIGGYPKGRII 58

Query: 71  EIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHALDSIYARKLGVDLKNLLISQPDTG 130
           EIYGPESSGKTTLALH IA++QK GGT AF+DAEHALD +YA+KLGVDL NLLISQPDTG
Sbjct: 59  EIYGPESSGKTTLALHAIAEAQKLGGTVAFIDAEHALDPVYAKKLGVDLDNLLISQPDTG 118

Query: 131 EQALEITDMLVRSGAVDIIVIDSVAALTPRAEIEGDMGESLPGMQARLMSQALRKLTSSI 190
           EQALEI D LVRSGAVD+IV+DSVAAL P+AEIEG+MG+S  G+QARLMSQALRKLT SI
Sbjct: 119 EQALEIADSLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSI 178

Query: 191 SRSKCILVFINQMRMKIGVMFGSPETTTGGNALKFYSSVRLDIRRVGSIKDKDSITGNQT 250
           ++S   ++FINQ+R KIGVMFG+PETTTGGNALKFYSSVRLDIRR+ +IKD D + GN+T
Sbjct: 179 NKSNTTVIFINQLREKIGVMFGNPETTTGGNALKFYSSVRLDIRRIETIKDGDEVIGNRT 238

Query: 251 RVKVVKNKMASPFKQVEFDIMYGEGISFFGELIDLGVKASIVDKSGAWFSFKGQRLGQGR 310
           +VKVVKNK+A PFK  EFDI++GEGIS  GE+IDL V+  I+ KSG+W+S+  ++LGQGR
Sbjct: 239 KVKVVKNKVAPPFKTAEFDILFGEGISREGEIIDLAVELGIIKKSGSWYSYGDEKLGQGR 298

Query: 311 ENSKIFLRENIEIAENIESLLRQNAGL 337
           EN+K +L+EN E+A+ IE  +R+  GL
Sbjct: 299 ENAKEYLKENPELADEIEKKVREKLGL 325


>gnl|CDD|30816 COG0468, RecA, RecA/RadA recombinase [DNA replication,
           recombination, and repair].
          Length = 279

 Score =  296 bits (759), Expect = 6e-81
 Identities = 174/286 (60%), Positives = 213/286 (74%), Gaps = 12/286 (4%)

Query: 6   EMNIVDKSKALEAALSQIQRVYGKGAIMQLGSQGSIFEGIEVVSSGSLGLDIALGIGGFP 65
               +D+ KALEAAL+QI++ +GKG+IM LG      E IE +S+GSL LD ALG GG P
Sbjct: 1   MAQGIDEEKALEAALAQIEKAFGKGSIMALGGD-ERREDIEAISTGSLALDEALG-GGLP 58

Query: 66  KGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHALDSIYARKLGVD-LKNLLI 124
           +GRI EIYGPESSGKTTLAL  +A +QK GG  AF+D EHALD   A++LGVD L NLL+
Sbjct: 59  RGRITEIYGPESSGKTTLALQLVANAQKPGGKAAFIDTEHALDPERAKQLGVDLLDNLLV 118

Query: 125 SQPDTGEQALEITDMLVRSGA--VDIIVIDSVAALTPRAEIEGDMGESLPGMQARLMSQA 182
           SQPDTGEQ LEI + L RSGA  +D++V+DSVAAL    EIE    +   G++ARL+S+A
Sbjct: 119 SQPDTGEQQLEIAEKLARSGAEKIDLLVVDSVAALVRAEEIE----DGHLGLRARLLSKA 174

Query: 183 LRKLTSSISRSKCILVFINQMRMKIGVMFGSPETTTGGNALKFYSSVRLDIRRVGSIKDK 242
           LRKLT   ++    ++F NQ+R KIGVMFG PETTTGGNALKFY+SVRLD+RR+ S+K+ 
Sbjct: 175 LRKLTRLANKYNTAVIFTNQVRAKIGVMFGDPETTTGGNALKFYASVRLDLRRIESLKED 234

Query: 243 DSITGNQTRVKVVKNKMASPFKQVEFDIMYGEGISFFGELIDLGVK 288
               GN+ RVKVVKNK+A PFK+ EFDI YG GI   GELIDLGVK
Sbjct: 235 ---VGNKRRVKVVKNKVAPPFKEAEFDITYGGGIDREGELIDLGVK 277


>gnl|CDD|30003 cd01393, recA_like, RecA is a  bacterial enzyme which has roles in
           homologous recombination, DNA repair, and the induction
           of the SOS response.  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..
          Length = 226

 Score =  235 bits (601), Expect = 2e-62
 Identities = 97/238 (40%), Positives = 126/238 (52%), Gaps = 29/238 (12%)

Query: 48  VSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQKTG------GTCAFV 101
           +S+GS  LD  LG GG P GRI EI+G   SGKT L L    ++Q  G      G   ++
Sbjct: 1   ISTGSKALDELLG-GGIPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYI 59

Query: 102 DAEHALDSIYARKLGVD--------LKNLLISQPDTGEQALEITDMLVR---SGAVDIIV 150
           D E A       +L V         L N+ +++P  GEQ LEI + L R   SG VD++V
Sbjct: 60  DTEGAFRPERLVQLAVRFGLDPEEVLDNIYVARPYNGEQQLEIVEELERIMSSGRVDLVV 119

Query: 151 IDSVAALTPRAEIEGDMGESLPGMQARLMSQALRKLTSSISRSKCILVFINQMRMKIGVM 210
           +DSVAAL  +  I   M       +ARL+SQALRKL     +    +VF NQ+R K+ VM
Sbjct: 120 VDSVAALFRKEFIGRGM----LAERARLLSQALRKLLRLADKFNVAVVFTNQVRAKVDVM 175

Query: 211 FGSPETTTGGNALKFYSSVRLDIRRVGSIKDKDSITGNQTRVKVVKNKMASPFKQVEF 268
           FG PET  GGNAL   S+ RLD+R+         I G +   KVVK+  A P  + EF
Sbjct: 176 FGDPETPAGGNALAHASTTRLDLRKGR------GIIGERRIAKVVKSP-ALPEAEAEF 226


>gnl|CDD|36646 KOG1433, KOG1433, KOG1433, DNA repair protein RAD51/RHP55
           [Replication, recombination and repair].
          Length = 326

 Score =  131 bits (330), Expect = 4e-31
 Identities = 66/334 (19%), Positives = 115/334 (34%), Gaps = 20/334 (5%)

Query: 7   MNIVDKSKALEAALSQIQRVYGKGAIMQLGSQGSI-FEGIEVVSSGSLGLDIALGIGGFP 65
           M +  K  AL+ AL +I       A ++    G I  E + ++S G L     L   G  
Sbjct: 1   MRMSQKRLALQKALEEIG---LSPAPVRFLLAGGITAEDVLLLSEGELSTVEGLAYAGKE 57

Query: 66  KGRIVEIYGPESSGKTTLALHTIAQS-QKTGGTCAFVDAEHALDSIYARKLGVDLKNLLI 124
           +  ++       SGKT L LH +    Q             ALD +    +       L+
Sbjct: 58  ELLLIIGLSEAKSGKTVLGLHKLVPMLQLRSELGFLSTGSKALDKLLGGGIETGSLTELV 117

Query: 125 SQPDTGEQALEITD-MLVRSGAVDIIVIDSVA--ALTPRAEIEGDMGESLPGMQARLMSQ 181
             P +G+  L  T  +    G   ++ ID+ +   L    EI G  G       + LM  
Sbjct: 118 GPPGSGKTQLCHTLAVTCGGGEGKVLYIDTESTFRLERLTEIAGRSGLRGRDTLSNLMLA 177

Query: 182 ALRKLTSSISRSKCILVFINQMRMKIGVM--FGSPETTTGGNALKFYSSVRLDIRRVGSI 239
               L   +   +   + INQ R+K+ ++    +   TT     +  +   L  + + S+
Sbjct: 178 RAYNLDHQLQLIQEAEIMINQSRVKLLIVDSATALYRTTFKGRGELSARQMLLAKFLRSL 237

Query: 240 KDKDSITGNQTRVKVVKNKMASPFKQVEFDIMYGEGISFFGELIDLGVKASIVDKSGAWF 299
           K      G      V+ N++ +        IM+G        +       ++  + G   
Sbjct: 238 KKLADEFGVAV---VITNQVTAQVDGA---IMFGS--DPKKPIGGNIWAHAVTTRLGLRK 289

Query: 300 SFKGQRLGQGRENSKIFLRENIEIAENIESLLRQ 333
             KG+R    +      L E   +    E  +  
Sbjct: 290 G-KGERR-ICKIADSPCLPEAEAVFAITEDGISD 321


>gnl|CDD|29989 cd01123, Rad51_DMC1_radA, Rad51_DMC1_radA,B. 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 ..
          Length = 235

 Score = 74.1 bits (182), Expect = 6e-14
 Identities = 66/252 (26%), Positives = 107/252 (42%), Gaps = 39/252 (15%)

Query: 48  VSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQK------TGGTCAFV 101
           +++GS  LD  LG GG   G I EI+G   SGKT L        Q         G   ++
Sbjct: 1   LTTGSKALDELLG-GGIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYI 59

Query: 102 DAEHA-----LDSIYARKLGVDLKNLL----ISQPDTGEQALEITD----MLVRSGAVDI 148
           D E       L  I A + G+D + +L    +++    +  L++ +    +L+ S  + +
Sbjct: 60  DTEGTFRPERLVQI-AERFGLDPEEVLDNIYVARAYNSDHQLQLLEELEAILIESSRIKL 118

Query: 149 IVIDSVAALTPRAEIEGDMGESLPGMQARLMSQALRKLTSSISRSKCILVFINQMRMKIG 208
           +++DSV AL  RAE +G  GE     + + +++ LR L          +V  NQ+  +  
Sbjct: 119 VIVDSVTALF-RAEFDG-RGEL--AERQQHLAKLLRTLKRLADEFNVAVVITNQVTARPD 174

Query: 209 VM---FGSPETTTGGNALKFYSSVRLDIRRVGSIKDKDSITGNQTRVKVVKNKMASPFKQ 265
                 G P+   GGN     S+ RL +R+           G +   K+V +    P  +
Sbjct: 175 GAAMFGGDPKKPAGGNIWAHASTTRLYLRKGR---------GEERIAKIVDSPHL-PEGE 224

Query: 266 VEFDIMYGEGIS 277
             F I   EGI 
Sbjct: 225 AVFAI-TEEGIR 235


>gnl|CDD|29986 cd01120, RecA-like_NTPases, RecA-like NTPases. 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..
          Length = 165

 Score = 72.8 bits (178), Expect = 1e-13
 Identities = 40/175 (22%), Positives = 66/175 (37%), Gaps = 18/175 (10%)

Query: 69  IVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHALDSIYAR----KLGVDLKNLLI 124
           ++ ++GP  SGKTTLAL         GG   +VD E  ++ +  R     L   L NL+I
Sbjct: 1   LILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLII 60

Query: 125 SQPDTGEQALE----ITDMLVRSGAVDIIVIDSVAALTPRAEIEGDMGESLPGMQARLMS 180
                 + A        + L   G  D+I++D +  L           E   G     + 
Sbjct: 61  VFATADDPAAARLLSKAERLRERGGDDLIILDELTRLVRALR------EIREGYP-GELD 113

Query: 181 QALRKLTSSISRSKCILVFINQMRMKIGVMFGSPETTTGGNALKFYSSVRLDIRR 235
           + LR+L     +    ++F  Q+          P  T G   L+  +   + + R
Sbjct: 114 EELRELLERARKGGVTVIFTLQVPSGDKGD---PRLTRGAQNLEDIADTVIVLSR 165


>gnl|CDD|30004 cd01394, radB, RadB. The archaeal protein radB shares similarity
           radA, the archaeal functional homologue to the bacterial
           RecA. The precise function of radB is unclear..
          Length = 218

 Score = 62.3 bits (151), Expect = 2e-10
 Identities = 53/206 (25%), Positives = 90/206 (43%), Gaps = 32/206 (15%)

Query: 48  VSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHAL 107
           + +G  GLD  LG GG  +G + ++YGP  +GKT +A+    ++   G   A++D E   
Sbjct: 1   LPTGCKGLDELLG-GGVERGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYIDTEGLS 59

Query: 108 DSIYARKLGVD----LKNLLISQP-DTGEQALEITDM--LVRSGAVDIIVIDSVAALTPR 160
              + +  G        ++++ +P D  EQ   I +         VD++V+DS  AL  R
Sbjct: 60  SERFRQIAGDRPERAASSIIVFEPMDFNEQGRAIQETETFADE-KVDLVVVDSATALY-R 117

Query: 161 AEIEGDMGESLPGMQARLMSQALRKLTSSIS-------RSKCILVFINQMRMKIGVMFGS 213
            E+  D              +  R+L   ++       +    +V  NQ+   +G     
Sbjct: 118 LELGDD----------DTTIKNYRELAKQLTFLLWLARKHDVAVVITNQVYSDVGSGSVR 167

Query: 214 PETTTGGNALKFYSSV--RLDIRRVG 237
           P    GG+ L+ +S V  RL+  RVG
Sbjct: 168 P---LGGHTLEHWSKVILRLEKLRVG 190


>gnl|CDD|30815 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
           transduction [Signal transduction mechanisms].
          Length = 260

 Score = 53.6 bits (128), Expect = 9e-08
 Identities = 56/262 (21%), Positives = 99/262 (37%), Gaps = 49/262 (18%)

Query: 45  IEVVSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAE 104
           +E + +G  GLD  LG GG P+G +V I GP  +GKT  AL  + +  + G    +V  E
Sbjct: 2   MERIPTGIPGLDEILG-GGLPRGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTE 60

Query: 105 HALDSIY--ARKLGVDLKNLL---------------------ISQPDTGEQALEITDMLV 141
            + + +   AR  G DL+  +                     +  P   E+ L+    +V
Sbjct: 61  ESPEELLENARSFGWDLEVYIEKGKLAILDAFLSEKGLVSIVVGDPLDLEELLDRIREIV 120

Query: 142 RSGAVDIIVIDSVAALTPRAEIEGDMGESLPGMQARLMSQALRKLTSSISRSKCILVFIN 201
                D +VIDS+  LT        +  + P +  R++      L   + +     +   
Sbjct: 121 EKEGADRVVIDSITELT--------LYLNDPALVRRIL----LLLKRFLKKLGVTSLLTT 168

Query: 202 QMRMKIGVMFGSPETTTGGNALKFYSSVRLDIRRVGSIKDKDSITGNQTRVKVVKNKMAS 261
           +  +            +G         +RLD++ +    D+  +   + R      K+  
Sbjct: 169 EAPV-------EERGESGVEEYIVDGVIRLDLKEIEGGGDRRYLRILKMRGTPHSLKV-- 219

Query: 262 PFKQVEFDIMYGEGISFFGELI 283
               + F+I  GEGI  + E  
Sbjct: 220 ----IPFEITDGEGIVVYPEGR 237


>gnl|CDD|29987 cd01121, Sms, Sms (bacterial radA) DNA repair protein. 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..
          Length = 372

 Score = 47.9 bits (114), Expect = 4e-06
 Identities = 36/114 (31%), Positives = 54/114 (47%), Gaps = 7/114 (6%)

Query: 43  EGIEVVSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVD 102
           E  E + +G   LD  LG GG   G ++ I G    GK+TL L   A+  K GG   +V 
Sbjct: 59  EEEERIPTGIEELDRVLG-GGLVPGSVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVS 117

Query: 103 AEHALDSI--YARKLGVDLKNLLISQPDTGEQALEITDMLVRSGAVDIIVIDSV 154
            E + + I   A +LG+  +NL +      E  LE     +     D+++IDS+
Sbjct: 118 GEESPEQIKLRADRLGISTENLYL----LAETNLEDILASIEELKPDLVIIDSI 167


>gnl|CDD|36777 KOG1564, KOG1564, KOG1564, DNA repair protein RHP57 [Replication,
           recombination and repair].
          Length = 351

 Score = 47.7 bits (113), Expect = 5e-06
 Identities = 42/186 (22%), Positives = 69/186 (37%), Gaps = 33/186 (17%)

Query: 46  EVVSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQ------KTGGTCA 99
             +++G + LD  L  GG P   I EI G    GKT L L      Q        GG   
Sbjct: 82  SKLTTGCVALDECLR-GGIPTDGITEICGESGCGKTQLLLQLSLCVQLPRSHGGLGGGAV 140

Query: 100 FVDAE--------HALDSIYARKLGVDLKNLLISQPDTG---------EQALEITD---- 138
           ++  E        H L     ++   + +      P            +  L I +    
Sbjct: 141 YICTESPFPTRRLHQLSHTLPQRPNPEKELNYNDNPGDHIFVENVHDVDHLLHIVNRQLP 200

Query: 139 MLVRSGAVDIIVIDSVAALTPRAEIEGDMGESLP-GMQARLMSQALRKLTSSISRSKCIL 197
           +L+    + +++IDSVAAL  R+E + +  +          ++  LR+L S        +
Sbjct: 201 ILLNRKKIKLVIIDSVAALF-RSEFDYNPSDLKKRARHLFRLAGKLRQLASKFD---LAV 256

Query: 198 VFINQM 203
           V  NQ+
Sbjct: 257 VCANQV 262


>gnl|CDD|31265 COG1066, Sms, Predicted ATP-dependent serine protease
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 456

 Score = 47.1 bits (112), Expect = 8e-06
 Identities = 44/143 (30%), Positives = 63/143 (44%), Gaps = 16/143 (11%)

Query: 48  VSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHAL 107
           +S+G   LD  LG GG   G ++ I G    GK+TL L   A+  K  G   +V  E +L
Sbjct: 75  ISTGIEELDRVLG-GGLVPGSVILIGGDPGIGKSTLLLQVAARLAKR-GKVLYVSGEESL 132

Query: 108 DSIYAR--KLGVDLKNLLISQPDTGEQALEITDMLVRSGAVDIIVIDSVAALTPRAEIEG 165
             I  R  +LG+   NL +      E  LE     +     D++VIDS+  L        
Sbjct: 133 QQIKLRADRLGLPTNNLYL----LAETNLEDIIAELEQEKPDLVVIDSIQTLY------S 182

Query: 166 DMGESLPG--MQARLMSQALRKL 186
           +   S PG   Q R ++  L +L
Sbjct: 183 EEITSAPGSVSQVREVAAELMRL 205


>gnl|CDD|36647 KOG1434, KOG1434, KOG1434, Meiotic recombination protein Dmc1
           [Energy production and conversion, Replication,
           recombination and repair].
          Length = 335

 Score = 46.5 bits (110), Expect = 1e-05
 Identities = 58/210 (27%), Positives = 94/210 (44%), Gaps = 28/210 (13%)

Query: 48  VSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQK-------TGGTCAF 100
           +++GS  LD  LG GG P   I EI+G    GKT L+ HT+  + +        GG   F
Sbjct: 97  ITTGSSALDDILG-GGIPSMSITEIFGEFRCGKTQLS-HTLCVTVQLPREMGGVGGKAIF 154

Query: 101 VDAEHAL--DSI--YARKLGVD----LKNLLISQPDTGEQALEITDML----VRSGAVDI 148
           +D E     D I   A +  VD    L N+L  +    E+ +E+  +L       G   +
Sbjct: 155 IDTEGTFRPDRIKDIAERFKVDPDFTLDNILYFRAYNSEEQMELVYLLGDFLSEHGKYRL 214

Query: 149 IVIDSVAALTPRAEIEGDMGESLPGMQARLMSQALRKLTSSISRSKCILVFINQMRMKIG 208
           +++DS+ AL  R + +G    S    + + ++Q L+KL          +   NQ+    G
Sbjct: 215 VIVDSIMALF-RVDYDGRGELSE---RQQKLNQMLQKLNKLAEEFNVAVFLTNQVTTDPG 270

Query: 209 --VMFGS-PETTTGGNALKFYSSVRLDIRR 235
             + F S      GG++    S+ RL +R+
Sbjct: 271 AGMTFASQDLKPAGGHSWAHASTTRLILRK 300


>gnl|CDD|32701 COG2874, FlaH, Predicted ATPases involved in biogenesis of archaeal
           flagella [Cell motility and secretion / Intracellular
           trafficking and secretion].
          Length = 235

 Score = 35.2 bits (81), Expect = 0.026
 Identities = 30/142 (21%), Positives = 56/142 (39%), Gaps = 18/142 (12%)

Query: 39  GSIFEGIEVVSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTC 98
             + E  +++ SG+  LD  LG GG P G ++ I G   +GK+ L+          G   
Sbjct: 1   MMVEELKKIIKSGNDELDKRLG-GGIPVGSLILIEGDNGTGKSVLSQRFAYGFLMNGYRV 59

Query: 99  AFVDAEHALDSIYAR--KLGVDLKNLLISQ---------------PDTGEQALEITDMLV 141
            +V  E  +     +   L  D+ + L+S                  +  + L++    +
Sbjct: 60  TYVSTELTVREFIKQMESLSYDVSDFLLSGRLLFFPVNLEPVNWGRRSARKLLDLLLEFI 119

Query: 142 RSGAVDIIVIDSVAALTPRAEI 163
           +    D+I+IDS++A       
Sbjct: 120 KRWEKDVIIIDSLSAFATYDSE 141


>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 = 35.2 bits (81), Expect = 0.029
 Identities = 25/136 (18%), Positives = 45/136 (33%), Gaps = 26/136 (19%)

Query: 65  PKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHALDSIYARKLGVDLKNLLI 124
           P  + + +YGP  +GKTTLA     +  + G    +++A              DL   L+
Sbjct: 17  PPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNAS-------------DLLEGLV 63

Query: 125 SQPDTGEQALEITDMLVRSGAVDIIVIDSVAALTPRAEIEGDMGESLPGMQARLMSQALR 184
                G   + +   L       ++ ID + +L+  A             Q  L+     
Sbjct: 64  VAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLSRGA-------------QNALLRVLET 110

Query: 185 KLTSSISRSKCILVFI 200
                I R    ++  
Sbjct: 111 LNDLRIDRENVRVIGA 126


>gnl|CDD|29990 cd01124, KaiC, KaiC is a circadian clock protein primarily found in
           cyanobacteria KaiC is a RecA-like ATPase, having both
           Walker A and Walker B motifs. A related protein is found
           in archaea..
          Length = 187

 Score = 34.9 bits (80), Expect = 0.036
 Identities = 36/168 (21%), Positives = 57/168 (33%), Gaps = 34/168 (20%)

Query: 69  IVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHALDSIY--ARKLGVDLK------ 120
              + G   +GKTT AL  +      G    +V  E + + +   A  LG DL+      
Sbjct: 1   STLLSGGPGTGKTTFALQFLYAGLARGEPGLYVTLEESPEELIENAESLGWDLERLEDEG 60

Query: 121 NLLISQPDTG-----------EQALEITDMLVRSGAVDIIVIDSVAALTPRAEIEGDMGE 169
            L I   D             E    + D +    A   +VIDSV+ L    +       
Sbjct: 61  LLAIVDADPDEIGPAESSLRLELIQRLKDAIEEFKA-KRVVIDSVSGLLLMEQS------ 113

Query: 170 SLPGMQARLMSQALRKLTSSISRSKCILVFINQMRMKIGVMFGSPETT 217
                 ARL    +R+L  ++ R     +  ++     G  FG  +  
Sbjct: 114 -----TARLE---IRRLLFALKRFGVTTLLTSEQSGLEGTGFGGGDVE 153


>gnl|CDD|29988 cd01122, GP4d_helicase, GP4d_helicase is a homohexameric 5'-3'
           helicases. Helicases couple NTP hydrolysis to the
           unwinding of nucleic acid duplexes into their component
           strands..
          Length = 271

 Score = 31.8 bits (72), Expect = 0.28
 Identities = 36/235 (15%), Positives = 73/235 (31%), Gaps = 49/235 (20%)

Query: 62  GGFPKGRIVEIYGPESSGKTTL----ALHTIAQSQKTGGTCAF----------------- 100
            G  KG ++ +      GKTT     AL  I Q     GT +                  
Sbjct: 25  KGLRKGELIILTAGTGVGKTTFLREYALDLITQHGVRVGTISLEEPVVRTARRLLGQYAG 84

Query: 101 ----------VDAEHALDSIYARKLGVDLKNLLISQPDTG-EQALEITDMLVRSGAVDII 149
                     +      D+ +    G     +  S  +   +  LE    +  S  +  I
Sbjct: 85  KRLHLPDTVFIYTLEEFDAAFDEFEGTGRLFMYDSFGEYSMDSVLEKVRYMAVSHGIQHI 144

Query: 150 VIDSVAALTPRAEIEGDMGESLPGMQARLMSQALRKLTSSISRSKCILVFINQMRM---K 206
           +ID+++ +       GD           +M+  LR      +     +  ++ +R     
Sbjct: 145 IIDNLSIMVSDERASGDE----RKALDEIMT-KLRGFA---TEHGIHITLVSHLRRPDGD 196

Query: 207 IGVMFGSPETTT---GGNALKFYSSVRLDIRRVGSIKDKDSITGNQTRVKVVKNK 258
                G   + +   G  A+   +   + + R    +  +    N T ++++KN+
Sbjct: 197 KTHEEGGEVSLSDFRGSAAIGQLADNVIALERN---QQAELDERNTTYLRILKNR 248


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

 Score = 31.9 bits (72), Expect = 0.29
 Identities = 22/99 (22%), Positives = 39/99 (39%), Gaps = 13/99 (13%)

Query: 72  IYGPESSGKTTLALHTI--AQSQKTGGTCAFVDAEHA--LDSIYARKLGVDLKNLLISQP 127
           IYGP  +GKT      +   +         +++         + ++     + N L   P
Sbjct: 47  IYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSK-----ILNKLGKVP 101

Query: 128 DTGEQALEITDMLVRS----GAVDIIVIDSVAALTPRAE 162
            TG+ +LEI   L  +    G   I+++D V AL  +  
Sbjct: 102 LTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDG 140


>gnl|CDD|30527 COG0178, UvrA, Excinuclease ATPase subunit [DNA replication,
          recombination, and repair].
          Length = 935

 Score = 31.7 bits (72), Expect = 0.30
 Identities = 13/31 (41%), Positives = 20/31 (64%), Gaps = 1/31 (3%)

Query: 64 FPKGRIVEIYGPESSGKTTLALHTI-AQSQK 93
           P+ ++V I G   SGK++LA  TI A+ Q+
Sbjct: 23 IPRNKLVVITGLSGSGKSSLAFDTIYAEGQR 53


>gnl|CDD|34201 COG4559, COG4559, ABC-type hemin transport system, ATPase component
           [Inorganic ion transport and metabolism].
          Length = 259

 Score = 31.8 bits (72), Expect = 0.33
 Identities = 27/142 (19%), Positives = 52/142 (36%), Gaps = 7/142 (4%)

Query: 64  FPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAF--VDAEHALDSIYARKLGVDLKN 121
              G ++ I GP  +GK+TL      +     G      V          AR   V  +N
Sbjct: 24  LRPGEVLAILGPNGAGKSTLLKALSGELSPDSGEVTLNGVPLNSWPPEELARHRAVLPQN 83

Query: 122 LLISQPDTGEQALEITDMLVRSGAVDIIVIDSVAALTPRAEIEGDMGESLP----GMQAR 177
             ++ P T ++ +++  +  RSG          A      ++ G  G        G Q R
Sbjct: 84  SSLAFPFTVQEVVQMGRIPHRSGREPEEDERIAAQALAATDLSGLAGRDYRTLSGGEQQR 143

Query: 178 L-MSQALRKLTSSISRSKCILV 198
           + +++ L +L   +   + + +
Sbjct: 144 VQLARVLAQLWPPVPSGRWLFL 165


>gnl|CDD|30727 COG0378, HypB, Ni2+-binding GTPase involved in regulation of
           expression and maturation of urease and hydrogenase
           [Posttranslational modification, protein turnover,
           chaperones / Transcription].
          Length = 202

 Score = 31.7 bits (72), Expect = 0.33
 Identities = 21/101 (20%), Positives = 38/101 (37%), Gaps = 9/101 (8%)

Query: 68  RIVEIYGPESSGKTTLALHTIAQSQK-------TGGTCAFVDAEHALDSIYARKLGVDLK 120
             + + GP  SGKT L   T+   +        TG      DA+          +GV+  
Sbjct: 14  LRIGVGGPPGSGKTALIEKTLRALKDEYKIAVITGDIYTKEDADRLRKLPGEPIIGVETG 73

Query: 121 NLLISQPDTGEQALEITDMLVRSGAVDIIVIDSVAALTPRA 161
                      +A+E  ++++    +D++ I+SV  L    
Sbjct: 74  KGCHLDASMNLEAIE--ELVLDFPDLDLLFIESVGNLVCPF 112


>gnl|CDD|145008 pfam01637, Arch_ATPase, Archaeal ATPase.  This family contain a
           conserved P-loop motif that is involved in binding ATP.
           This family is almost exclusively found in
           archaebacteria and particularly in Methanococcus
           jannaschii that encodes sixteen members of this family.
          Length = 223

 Score = 31.5 bits (72), Expect = 0.38
 Identities = 22/94 (23%), Positives = 37/94 (39%), Gaps = 10/94 (10%)

Query: 68  RIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDA-----EHALDSIY-----ARKLGV 117
            I+ +YGP   GKT L    + + ++ G    + D      E  LD        A  LG 
Sbjct: 21  PIIVVYGPRRCGKTALLREFLEELRELGYRVIYYDPLRREFEEKLDRFEEAKRLAEALGD 80

Query: 118 DLKNLLISQPDTGEQALEITDMLVRSGAVDIIVI 151
            L  + I++      +L +   L++     I +I
Sbjct: 81  ALPKIGIAKSKLAFLSLTLLFELLKRKGKKIAII 114


>gnl|CDD|38070 KOG2859, KOG2859, KOG2859, DNA repair protein, member of the
           recA/RAD51 family [Replication, recombination and
           repair].
          Length = 293

 Score = 31.6 bits (71), Expect = 0.39
 Identities = 25/82 (30%), Positives = 39/82 (47%), Gaps = 12/82 (14%)

Query: 67  GRIVEIYGPESSGKTTLALHTIAQ---SQKTGG---TCAFVDAEHALD------SIYARK 114
           G +VEI GP +SGKT +    +A     +K GG   +  F+D +H  D      S+  R 
Sbjct: 38  GTLVEISGPGNSGKTLVLQQLVAHCILPKKFGGLQWSVLFIDLDHKFDRLRLAKSLRHRL 97

Query: 115 LGVDLKNLLISQPDTGEQALEI 136
               +  ++ ++  T EQ  EI
Sbjct: 98  KQYSVGEVIAAKCPTEEQLEEI 119


>gnl|CDD|48448 cd03750, proteasome_alpha_type_2, proteasome_alpha_type_2. The 20S
           proteasome, multisubunit proteolytic complex, is the
           central enzyme of nonlysosomal protein degradation in
           both the cytosol and nucleus. It is composed of 28
           subunits arranged as four homoheptameric rings that
           stack on top of one another forming an elongated
           alpha-beta-beta-alpha cylinder with a central cavity.
           The proteasome alpha and beta subunits are members of
           the N-terminal nucleophile (Ntn)-hydrolase superfamily.
           Their N-terminal threonine residues are exposed as a
           nucleophile in peptide bond hydrolysis. Mammals have 7
           alpha and 7 beta proteasome subunits while archaea have
           one of each..
          Length = 227

 Score = 31.4 bits (71), Expect = 0.42
 Identities = 14/44 (31%), Positives = 27/44 (61%), Gaps = 4/44 (9%)

Query: 292 VDKSGAWFSFKGQRLGQGRENSKIFLR----ENIEIAENIESLL 331
           VD SG++F++K   +G+   N+K FL     E++E+ + I + +
Sbjct: 144 VDPSGSYFTWKATAIGKNYSNAKTFLEKRYNEDLELEDAIHTAI 187


>gnl|CDD|29985 cd00984, DnaB_C, DnaB helicase C terminal domain. The hexameric
           helicase DnaB unwinds the DNA duplex at the  chromosome
           replication fork. Although the mechanism by which DnaB
           both couples ATP hydrolysis to translocation along DNA
           and denatures the duplex is unknown, a change in the
           quaternary structure of the protein involving
           dimerization of the N-terminal domain has been observed
           and may occur during the enzymatic cycle. This
           C-terminal domain contains an ATP-binding site and is
           therefore probably the site of ATP hydrolysis..
          Length = 242

 Score = 31.3 bits (71), Expect = 0.44
 Identities = 29/107 (27%), Positives = 43/107 (40%), Gaps = 13/107 (12%)

Query: 61  IGGFPKGRIVEIYGPESSGKTTLALHTIAQS--QKTGGTCAFVDAEHALDSIYARKL--- 115
            GG   G ++ I    S GKT  AL+ IA++  +K G    F   E + + +  R L   
Sbjct: 7   TGGLQPGDLIIIAARPSMGKTAFALN-IAENIAKKQGKPVLFFSLEMSKEQLLQRLLASE 65

Query: 116 -GVDLKNLLISQ--PDTGEQALEITDMLVRSGAVDIIVIDSVAALTP 159
            G+ L  L       +  E+  E    L        I ID  ++LT 
Sbjct: 66  SGISLSKLRTGSLSDEDWERLAEAIGELKELP----IYIDDSSSLTV 108


>gnl|CDD|72984 cd03225, ABC_cobalt_CbiO_domain1, Domain I of the ABC component of
           a cobalt transport family found in bacteria, archaea,
           and eukaryota.  The transition metal cobalt is an
           essential component of many enzymes and must be
           transported into cells in appropriate amounts when
           needed.  This ABC transport system of the CbiMNQO family
           is involved in cobalt transport in association with the
           cobalamin (vitamin B12) biosynthetic pathways.  Most of
           cobalt (Cbi) transport systems possess a separate CbiN
           component, the cobalt-binding periplasmic protein, and
           they are encoded by the conserved gene cluster cbiMNQO. 
           Both the CbiM and CbiQ proteins are integral cytoplasmic
           membrane proteins, and the CbiO protein has the linker
           peptide and the Walker A and B motifs commonly found in
           the ATPase components of the ABC-type transport
           systems..
          Length = 211

 Score = 31.2 bits (71), Expect = 0.50
 Identities = 18/60 (30%), Positives = 22/60 (36%), Gaps = 2/60 (3%)

Query: 64  FPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAF--VDAEHALDSIYARKLGVDLKN 121
             KG  V I GP  SGK+TL          T G       D          RK+G+  +N
Sbjct: 24  IKKGEFVLIVGPNGSGKSTLLRLLNGLLGPTSGEVLVDGKDLTKLSLKELRRKVGLVFQN 83


>gnl|CDD|72973 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.  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..
          Length = 180

 Score = 31.2 bits (71), Expect = 0.51
 Identities = 14/30 (46%), Positives = 17/30 (56%), Gaps = 1/30 (3%)

Query: 64 FPKGRIVEIYGPESSGKTTLALHTIAQSQK 93
             G IV I GP  +GK+TL L T+A   K
Sbjct: 22 IEAGEIVGILGPNGAGKSTL-LKTLAGLLK 50


>gnl|CDD|73055 cd03296, ABC_CysA_sulfate_importer, Part of the ABC transporter
           complex cysAWTP involved in sulfate import.  Responsible
           for energy coupling to the transport system.  The
           complex is composed of two ATP-binding proteins (cysA),
           two transmembrane proteins (cysT and cysW), and a
           solute-binding protein (cysP).  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 = 239

 Score = 31.0 bits (70), Expect = 0.59
 Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 64  FPKGRIVEIYGPESSGKTTLALHTIAQ-SQKTGGTCAFVDAEHALDSIYARKLG 116
            P G +V + GP  SGKTTL L  IA   +   GT  F   +     +  R +G
Sbjct: 25  IPSGELVALLGPSGSGKTTL-LRLIAGLERPDSGTILFGGEDATDVPVQERNVG 77


>gnl|CDD|32985 COG3172, NadR, Predicted ATPase/kinase involved in NAD metabolism
          [Coenzyme metabolism].
          Length = 187

 Score = 30.7 bits (69), Expect = 0.67
 Identities = 10/17 (58%), Positives = 12/17 (70%)

Query: 68 RIVEIYGPESSGKTTLA 84
          + V I G ESSGK+TL 
Sbjct: 9  KTVAILGGESSGKSTLV 25


>gnl|CDD|73009 cd03250, ABCC_MRP_domain1, Domain 1 of the ABC subfamily C.  This
          family is also known as MRP (mulrtidrug
          resisitance-associated protein).  Some of the MRP
          members have five additional transmembrane segments in
          their N-terminas, but the function of these additional
          membrane-spanning domains is not clear.  The MRP was
          found in the multidrug-resisting lung cancer cell in
          which p-glycoprotein was not overexpressed. MRP exports
          glutathione by drug stimulation, as well as, certain
          substrates in conjugated forms with anions, such as
          glutathione, glucuronate, and sulfate..
          Length = 204

 Score = 30.4 bits (69), Expect = 0.72
 Identities = 13/34 (38%), Positives = 20/34 (58%)

Query: 64 FPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGT 97
           PKG +V I GP  SGK++L    + + +K  G+
Sbjct: 28 VPKGELVAIVGPVGSGKSSLLSALLGELEKLSGS 61


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

 Score = 30.5 bits (69), Expect = 0.74
 Identities = 15/30 (50%), Positives = 17/30 (56%), Gaps = 1/30 (3%)

Query: 64 FPKGRIVEIYGPESSGKTTLALHTIAQSQK 93
           PKG I  I GP  SGK+TL L  +A   K
Sbjct: 25 IPKGEITGILGPNGSGKSTL-LKCLAGLLK 53


>gnl|CDD|73029 cd03270, ABC_UvrA_I, The excision repair protein UvrA domain I;
          Nucleotide excision repair in eubacteria is a process
          that repairs DNA damage by the removal of a 12-13-mer
          oligonucleotide containing the lesion.  Recognition and
          cleavage of the damaged DNA is a multistep
          ATP-dependent reaction that requires the UvrA, UvrB,
          and UvrC proteins.  Both UvrA and UvrB are ATPases,
          with UvrA having two ATP binding sites, which have the
          characteristic signature of the family of ABC proteins,
          and UvrB having one ATP binding site that is
          structurally related to that of helicases..
          Length = 226

 Score = 30.5 bits (69), Expect = 0.75
 Identities = 13/31 (41%), Positives = 20/31 (64%), Gaps = 1/31 (3%)

Query: 64 FPKGRIVEIYGPESSGKTTLALHTI-AQSQK 93
           P+ ++V I G   SGK++LA  TI A+ Q+
Sbjct: 18 IPRNKLVVITGVSGSGKSSLAFDTIYAEGQR 48


>gnl|CDD|35288 KOG0065, KOG0065, KOG0065, Pleiotropic drug resistance proteins
           (PDR1-15), ABC superfamily [Secondary metabolites
           biosynthesis, transport and catabolism].
          Length = 1391

 Score = 30.6 bits (69), Expect = 0.75
 Identities = 29/132 (21%), Positives = 47/132 (35%), Gaps = 13/132 (9%)

Query: 62  GGFPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCA---FVDAEHALDSIYARKLGVD 118
           G F  G +  + G   +GKTTL L  +A  +KTGG       +         +AR  G  
Sbjct: 812 GAFKPGVLTALMGESGAGKTTL-LDVLAG-RKTGGYIEGDILISGFPKDQETFARVSGYV 869

Query: 119 LKNLLISQPDTGEQALEITDMLVRSGAVDI--------IVIDSVAALTPRAEIEGDMGES 170
            +  + S   T  ++L  +  L     V           VI+ +        + G  G  
Sbjct: 870 EQQDIHSPELTVRESLRFSAALRLPKEVSDEEKYEYVEEVIELLELKEYADALVGLPGSG 929

Query: 171 LPGMQARLMSQA 182
           L   Q + ++  
Sbjct: 930 LSTEQRKRLTIG 941


>gnl|CDD|73014 cd03255, ABC_MJ0796_Lo1CDE_FtsE, This family is comprised of MJ0796
           ATP-binding cassette, macrolide-specific ABC-type efflux
           carrier (MacAB), and proteins involved in cell division
           (FtsE), and release of liporoteins from the cytoplasmic
           membrane (LolCDE).  They are clustered together
           phylogenetically.  MacAB is an exporter that confers
           resistance to macrolides, while the LolCDE system is not
           a transporter at all.  An FtsE null mutants showed
           filamentous growth and appeared viable on high salt
           medium only, indicating a role for FtsE in cell division
           and/or salt transport.  The LolCDE complex catalyses the
           release of lipoproteins from the cytoplasmic membrane
           prior to their targeting to the outer membrane..
          Length = 218

 Score = 30.5 bits (69), Expect = 0.77
 Identities = 18/61 (29%), Positives = 25/61 (40%), Gaps = 8/61 (13%)

Query: 64  FPKGRIVEIYGPESSGKTTLALHTIAQSQK-TGGTCAFVD------AEHALDSIYARKLG 116
             KG  V I GP  SGK+TL L+ +    + T G            +E  L +   R +G
Sbjct: 27  IEKGEFVAIVGPSGSGKSTL-LNILGGLDRPTSGEVRVDGTDISKLSEKELAAFRRRHIG 85

Query: 117 V 117
            
Sbjct: 86  F 86


>gnl|CDD|31315 COG1118, CysA, ABC-type sulfate/molybdate transport systems, ATPase
           component [Inorganic ion transport and metabolism].
          Length = 345

 Score = 30.3 bits (68), Expect = 0.84
 Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 8/66 (12%)

Query: 56  DIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHALDS----IY 111
           DI+L I     G +V + GP  +GK+TL L  IA  +        ++     D     + 
Sbjct: 20  DISLDI---KSGELVALLGPSGAGKSTL-LRIIAGLETPDAGRIRLNGRVLFDVSNLAVR 75

Query: 112 ARKLGV 117
            RK+G 
Sbjct: 76  DRKVGF 81


>gnl|CDD|33754 COG3973, COG3973, Superfamily I DNA and RNA helicases [General
           function prediction only].
          Length = 747

 Score = 30.4 bits (68), Expect = 0.91
 Identities = 13/26 (50%), Positives = 18/26 (69%)

Query: 64  FPKGRIVEIYGPESSGKTTLALHTIA 89
           F K +I+ + G   SGKTT+ALH +A
Sbjct: 223 FEKNKILVVQGAAGSGKTTIALHRVA 248


>gnl|CDD|73020 cd03261, ABC_Org_Solvent_Resistant, ABC (ATP-binding cassette)
          transport system involved in resistant to organic
          solvents; 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 = 235

 Score = 30.1 bits (68), Expect = 0.92
 Identities = 11/34 (32%), Positives = 16/34 (47%)

Query: 64 FPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGT 97
            +G I+ I GP  SGK+TL    +   +   G 
Sbjct: 23 VRRGEILAIIGPSGSGKSTLLRLIVGLLRPDSGE 56


>gnl|CDD|30598 COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA
           replication, recombination, and repair].
          Length = 843

 Score = 30.3 bits (68), Expect = 0.92
 Identities = 18/53 (33%), Positives = 24/53 (45%), Gaps = 5/53 (9%)

Query: 65  PKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHA----LDSIYAR 113
              RI+ I GP   GK+T  L  +A         +FV AE A    +D I+ R
Sbjct: 605 GNRRIILITGPNMGGKSTY-LRQVALIVILAQIGSFVPAEKARIGIVDRIFTR 656


>gnl|CDD|31331 COG1136, SalX, ABC-type antimicrobial peptide transport system,
           ATPase component [Defense mechanisms].
          Length = 226

 Score = 30.1 bits (68), Expect = 0.97
 Identities = 14/38 (36%), Positives = 17/38 (44%), Gaps = 2/38 (5%)

Query: 64  FPKGRIVEIYGPESSGKTTLALHTIAQSQK-TGGTCAF 100
              G  V I GP  SGK+TL L+ +    K T G    
Sbjct: 28  IEAGEFVAIVGPSGSGKSTL-LNLLGGLDKPTSGEVLI 64


>gnl|CDD|30201 cd02028, UMPK_like, Uridine monophosphate kinase_like (UMPK_like)
           is a family of proteins highly similar to the uridine
           monophosphate kinase (UMPK, EC 2.7.1.48), also known as
           uridine kinase or uridine-cytidine kinase (UCK)..
          Length = 179

 Score = 30.3 bits (68), Expect = 1.0
 Identities = 29/146 (19%), Positives = 44/146 (30%), Gaps = 32/146 (21%)

Query: 69  IVEIYGPESSGKTTLALHTIAQSQKTGGTCAFV----------DAEHALDSIY--ARKLG 116
           +V I GP  SGKTT A   ++   +  G    V                D  Y     L 
Sbjct: 1   VVGIAGPSGSGKTTFA-KKLSNQLRVNGIGPVVISLDDYYVPRKTPRDEDGNYDFESILD 59

Query: 117 VDLKNLLISQPDTG-EQALEITDMLVRSG---------AVDIIVIDSVAALTPRAEIEGD 166
           +DL N  +     G E  L I D                  +++++ + AL  R      
Sbjct: 60  LDLLNKNLHDLLNGKEVELPIYDFRTGKRRGYRKLKLPPSGVVILEGIYALNERLR---- 115

Query: 167 MGESLPGMQARLMSQALRKLTSSISR 192
                  +  R+       L   + R
Sbjct: 116 -----SLLDIRVAVSGGVHLNRLLRR 136


>gnl|CDD|73002 cd03243, ABC_MutS_homologs, The MutS protein initiates DNA mismatch
           repair by recognizing mispaired and unpaired bases
           embedded in duplex DNA and activating endo- and
           exonucleases to remove the mismatch.  Members of the
           MutS family also possess a conserved ATPase activity
           that belongs to the ATP binding cassette (ABC)
           superfamily.  MutS homologs (MSH) have been identified
           in most prokaryotic and all eukaryotic organisms
           examined.  Prokaryotes have two homologs (MutS1 and
           MutS2), whereas seven MSH proteins (MSH1 to MSH7) have
           been identified in eukaryotes.  The homodimer MutS1 and
           heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily
           involved in mitotic mismatch repair, whereas MSH4-MSH5
           is involved in resolution of Holliday junctions during
           meiosis.  All members of the MutS family contain the
           highly conserved Walker A/B ATPase domain, and many
           share a common mechanism of action.  MutS1, MSH2-MSH3,
           MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding
           clamps, and recognition of specific DNA structures or
           lesions results in ADP/ATP exchange..
          Length = 202

 Score = 30.2 bits (68), Expect = 1.0
 Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 5/54 (9%)

Query: 64  FPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHA----LDSIYAR 113
              GR++ I GP   GK+T  L +I  +        FV AE A    +D I+ R
Sbjct: 26  LGSGRLLLITGPNMGGKSTY-LRSIGLAVLLAQIGCFVPAESASIPLVDRIFTR 78


>gnl|CDD|38335 KOG3125, KOG3125, KOG3125, Thymidine kinase [Nucleotide transport
           and metabolism].
          Length = 234

 Score = 30.0 bits (67), Expect = 1.1
 Identities = 27/91 (29%), Positives = 38/91 (41%), Gaps = 9/91 (9%)

Query: 66  KGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFV----DAEHALDSIYARKLGVDLKN 121
           +G I  I GP  SGKTT  L  I +    G     +    D  +   SI     G+++  
Sbjct: 26  RGTIHVILGPMFSGKTTELLRRIRREIIAGRRVLLIKYAKDTRYESSSIVTHD-GIEMPC 84

Query: 122 LLISQPDTGEQALEITDMLVRSGAVDIIVID 152
             +  PD    +    D L  +G VD+I ID
Sbjct: 85  WAL--PDASFLSEFGKDAL--NGDVDVIGID 111


>gnl|CDD|72971 cd00267, ABC_ATPase, ABC (ATP-binding cassette) transporter
           nucleotide-binding domain; ABC transporters are a large
           family of proteins involved in the transport of a wide
           variety of different compounds, like sugars, ions,
           peptides, and more complex organic molecules.  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 = 157

 Score = 29.9 bits (67), Expect = 1.1
 Identities = 21/103 (20%), Positives = 39/103 (37%), Gaps = 8/103 (7%)

Query: 64  FPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHALDSIYARKLGVDLKNLL 123
              G IV + GP  SGK+TL        + T G       + A   +   +  +      
Sbjct: 22  LKAGEIVALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEELRRRI----GY 77

Query: 124 ISQPDTGE-QALEITDMLVRSGAVDIIVIDSV-AALTPRAEIE 164
           + Q   G+ Q + +   L+     D++++D   + L P +   
Sbjct: 78  VPQLSGGQRQRVALARALLL--NPDLLLLDEPTSGLDPASRER 118


>gnl|CDD|72892 cd03672, Dcp2p, mRNA decapping enzyme 2 (Dcp2p), the catalytic
           subunit, and Dcp1p are the two components of the
           decapping enzyme complex. Decapping is a key step in
           both general and nonsense-mediated 5'->3' mRNA-decay
           pathways. Dcp2p contains an all-alpha helical N-terminal
           domain and a C-terminal domain which has the Nudix fold.
           While decapping is not dependent on the N-terminus of
           Dcp2p, it does affect its efficiency. Dcp1p binds the
           N-terminal domain of Dcp2p stimulating the decapping
           activity of Dcp2p. Decapping permits the degradation of
           the transcript and is a site of numerous control inputs.
           It is responsible for nonsense-mediated decay as well as
           AU-rich element (ARE)-mediated decay. In addition, it
           may also play a role in the levels of mRNA. Enzymes
           belonging to the Nudix superfamily require a divalent
           cation, such as Mg2+ or Mn2+, for their activity and are
           recognized by a highly conserved 23-residue nudix motif
           (GX5EX7REUXEEXGU, where U = I, L or V)..
          Length = 145

 Score = 29.8 bits (67), Expect = 1.1
 Identities = 18/81 (22%), Positives = 31/81 (38%), Gaps = 9/81 (11%)

Query: 186 LTSSISRSKCILVFINQMRMKIGVMFGSPETTTGGNALKFYSSVRLDIRRVG--SIKDKD 243
           ++  I +   I + I    +K+ ++ G PE T       F    R +I ++    IKD  
Sbjct: 56  ISKYIDKDDYIELIIRGQNVKLYIVPGVPEDT------PFEPKTRKEISKIEWFDIKDLP 109

Query: 244 SITGNQTRVKV-VKNKMASPF 263
           +    +       K  M  PF
Sbjct: 110 TKKNKKIPGLNSNKFFMVIPF 130


>gnl|CDD|72993 cd03234, ABCG_White, The White subfamily represents ABC
          transporters homologous to the Drosophila white gene,
          which acts as a dimeric importer for eye pigment
          precursors.  The eye pigmentation of Drosophila is
          developed from the synthesis and deposition in the
          cells of red pigments, which are synthesized from
          guanine, and brown pigments, which are synthesized from
          tryptophan.  The pigment precursors are encoded by the
          white, brown, and scarlet genes, respectively.
          Evidence from genetic and biochemical studies suggest
          that the White and Brown proteins function as
          heterodimers to import guanine, while the White and
          Scarlet proteins function to import tryptophan.
          However, a recent study also suggests that White may be
          involved in the transport of a metabolite, such as
          3-hydroxykynurenine, across intracellular membranes.
          Mammalian ABC transporters belonging to the White
          subfamily (ABCG1, ABCG5, and ABCG8) have been shown to
          be involved in the regulation of lipid-trafficking
          mechanisms in macrophages, hepatocytes, and intestinal
          mucosa cells.  ABCG1 (ABC8), the human homolog of the
          Drosophila white gene is induced in monocyte-derived
          macrophages during cholesterol influx mediated by
          acetylated low-density lipoprotein.  It is possible
          that human ABCG1 forms heterodimers with several
          heterologous partners..
          Length = 226

 Score = 29.8 bits (67), Expect = 1.3
 Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 1/34 (2%)

Query: 64 FPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGT 97
             G+++ I G   SGKTTL L  I+   + GGT
Sbjct: 30 VESGQVMAILGSSGSGKTTL-LDAISGRVEGGGT 62


>gnl|CDD|30132 cd01516, FBPase_glpX, Bacterial fructose-1,6-bisphosphatase,
           glpX-encoded. A dimeric enzyme dependent on Mg(2+).
           glpX-encoded FPBase (FBPase class II) differs from other
           members of the inositol-phosphatase superfamily by
           permutation of secondary structure elements. The core
           structure around the active site is well preserved. In
           E. coli, FBPase II is part of the glp regulon, which
           mediates growth on glycerol or sn-glycerol 3-phosphate
           as the sole carbon source..
          Length = 309

 Score = 29.4 bits (66), Expect = 1.6
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 23  IQRVYGKGAIMQLGSQGSIFEGIEVVSSGSLGLDIALGIGGFPKGRI 69
           I+ +   GA ++L   G +   I     GS G+D+ +GIGG P+G +
Sbjct: 170 IEEIREAGARIKLIPDGDVAAAIATALPGS-GVDVLMGIGGAPEGVL 215


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

 Score = 29.4 bits (66), Expect = 1.8
 Identities = 11/46 (23%), Positives = 18/46 (39%)

Query: 64  FPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHALDS 109
             +G  + + G   SGK+TLA         + G+  F   +  L  
Sbjct: 314 LREGETLGLVGESGSGKSTLARILAGLLPPSSGSIIFDGQDLDLTG 359


>gnl|CDD|33632 COG3840, ThiQ, ABC-type thiamine transport system, ATPase component
           [Coenzyme metabolism].
          Length = 231

 Score = 29.1 bits (65), Expect = 1.8
 Identities = 17/51 (33%), Positives = 21/51 (41%), Gaps = 2/51 (3%)

Query: 64  FPKGRIVEIYGPESSGKTTLALHTIAQ-SQKTGGTCAFVDAEHALDSIYAR 113
            P G IV I GP  +GK+TL L+ IA       G       +H       R
Sbjct: 22  VPAGEIVAILGPSGAGKSTL-LNLIAGFETPASGEILINGVDHTASPPAER 71


>gnl|CDD|39152 KOG3949, KOG3949, KOG3949, RNA polymerase II elongator complex,
          subunit ELP4 [Chromatin structure and dynamics,
          Transcription].
          Length = 360

 Score = 29.2 bits (65), Expect = 1.8
 Identities = 16/40 (40%), Positives = 18/40 (45%), Gaps = 1/40 (2%)

Query: 33 MQLGSQGSIFEGIEVVSSGSLGLDIALGIGGFPKGRIVEI 72
             G + S   G  + SSG   LD  LG GG P G  V I
Sbjct: 14 SIAGVRPSPKNGQLITSSGIADLDQILG-GGLPLGSSVLI 52


>gnl|CDD|143485 cd06810, PLPDE_III_ODC_DapDC_like, Type III Pyridoxal 5-phosphate
           (PLP)-Dependent Enzymes, Ornithine and Diaminopimelate
           Decarboxylases, and Related Enzymes.  This family
           includes eukaryotic ornithine decarboxylase (ODC, EC
           4.1.1.17), diaminopimelate decarboxylase (DapDC, EC
           4.1.1.20), plant and prokaryotic biosynthetic arginine
           decarboxylase (ADC, EC 4.1.1.19), carboxynorspermidine
           decarboxylase (CANSDC), and ODC-like enzymes from
           diverse bacterial species. These proteins are fold type
           III PLP-dependent enzymes that catalyze essential steps
           in the  biosynthesis of polyamine and lysine. ODC and
           ADC participate in alternative pathways of the
           biosynthesis of putrescine, which is the precursor of
           aliphatic polyamines in many organisms. ODC catalyzes
           the direct synthesis of putrescine from L-ornithine,
           while ADC converts L-arginine to agmatine, which is
           hydrolysed to putrescine by agmatinase in a pathway that
           exists only in plants and bacteria. DapDC converts
           meso-2,6-diaminoheptanedioate to L-lysine, which is the
           final step of lysine biosynthesis. CANSDC catalyzes the
           decarboxylation of carboxynorspermidine, which is the
           last step in the synthesis of norspermidine. The
           PLP-dependent decarboxylases in this family contain an
           N-terminal PLP-binding TIM-barrel domain and a
           C-terminal beta-sandwich domain, similar to bacterial
           alanine racemases. They exist as homodimers with active
           sites that lie at the interface between the TIM barrel
           domain of one subunit and the beta-sandwich domain of
           the other subunit. Prokaryotic ornithine, lysine and
           biodegradative arginine decarboxylases are fold type I
           PLP-dependent enzymes and are not included in this
           family.
          Length = 368

 Score = 29.2 bits (66), Expect = 2.0
 Identities = 46/215 (21%), Positives = 84/215 (39%), Gaps = 35/215 (16%)

Query: 9   IVDKSKALEAAL-SQIQRVYG-KG----AIMQ-LGSQGSIFEGIEVVSSGSLGLDIALGI 61
           I     AL+ AL S ++  Y  K      +++ L   G    G +V S G   L +AL  
Sbjct: 11  IRAHYAALKEALPSGVKLFYAVKANPNPHVLRTLAEAG---TGFDVASKGE--LALALAA 65

Query: 62  GGFPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAF-VDAEHALDSI--YARKLGVD 118
           G  P+ RI+   GP    K+   +     S    G     VD+   L+ +   A+KLG  
Sbjct: 66  GVPPE-RII-FTGP---AKSVSEIEAALAS----GVDHIVVDSLDELERLNELAKKLGPK 116

Query: 119 LKNLLISQPDTGEQALEI--TDMLVRSGAVDIIVIDSVAALTPRAEIEGDMGESLPGMQA 176
            + LL   PD      +I    +  + G + +    +        ++       L G+  
Sbjct: 117 ARILLRVNPDVSAGTHKISTGGLKSKFG-LSLSEARAALERAKELDL------RLVGLHF 169

Query: 177 RLMSQALR--KLTSSISRSKCILVFINQMRMKIGV 209
            + SQ L    +  ++S ++ ++  + +M   + +
Sbjct: 170 HVGSQILDLETIVQALSDARELIEELVEMGFPLEM 204


>gnl|CDD|73018 cd03259, ABC_Carb_Solutes_like, ABC Carbohydrate and Solute
          Transporters-like subgroup.  This family is comprised
          of proteins involved in the transport of apparently
          unrelated solutes and proteins specific for di- and
          oligosaccharides and polyols.  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 = 213

 Score = 28.9 bits (65), Expect = 2.0
 Identities = 11/26 (42%), Positives = 13/26 (50%), Gaps = 1/26 (3%)

Query: 64 FPKGRIVEIYGPESSGKTTLALHTIA 89
             G  + + GP   GKTTL L  IA
Sbjct: 23 VEPGEFLALLGPSGCGKTTL-LRLIA 47


>gnl|CDD|33398 COG3598, RepA, RecA-family ATPase [DNA replication, recombination,
           and repair].
          Length = 402

 Score = 28.8 bits (64), Expect = 2.2
 Identities = 37/168 (22%), Positives = 62/168 (36%), Gaps = 44/168 (26%)

Query: 64  FPKGRIVEIYGPESSGKTTLALHT----------IAQSQKTGGTCAFVDAE-------HA 106
           F KG +  +YG    GKTTL L+                K  G   +V  E         
Sbjct: 86  FRKGYVSILYGDSGVGKTTLLLYLCIALAAGKNLFGNKVKEPGKVLYVSLELYREDILER 145

Query: 107 LDSIYARKLGV---DLKNLLI---SQPDTGEQALEITDMLVRSGAVDI-------IVIDS 153
           L+ + AR +G+   D++N+ +   S        L     L R     +       +VID 
Sbjct: 146 LEPVRAR-MGLSPADVRNMDLTDVSGAADESDVLS--PKLYRRFEKILEQKRPDFVVIDP 202

Query: 154 VAALTPRAEIEGDMGESLPGMQARLMSQALRKLTSSISRSKCILVFIN 201
             A           G+S+  +Q +   +  RKL  +    +C +++I+
Sbjct: 203 FVAFY--------EGKSISDVQVKEFIKKTRKLARN---LECAIIYIH 239


>gnl|CDD|33633 COG3842, PotA, ABC-type spermidine/putrescine transport systems,
           ATPase components [Amino acid transport and metabolism].
          Length = 352

 Score = 28.7 bits (64), Expect = 2.4
 Identities = 21/63 (33%), Positives = 27/63 (42%), Gaps = 5/63 (7%)

Query: 56  DIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQ-SQKTGGTCAFVDAEHALDSIYARK 114
           DI+L I    KG  V + GP   GKTTL L  IA   Q + G       +        R 
Sbjct: 23  DISLDI---KKGEFVTLLGPSGCGKTTL-LRMIAGFEQPSSGEILLDGEDITDVPPEKRP 78

Query: 115 LGV 117
           +G+
Sbjct: 79  IGM 81


>gnl|CDD|72997 cd03238, ABC_UvrA, The excision repair protein UvrA; Nucleotide
          excision repair in eubacteria is a process that repairs
          DNA damage by the removal of a 12-13-mer
          oligonucleotide containing the lesion.  Recognition and
          cleavage of the damaged DNA is a multistep
          ATP-dependent reaction that requires the UvrA, UvrB,
          and UvrC proteins.  Both UvrA and UvrB are ATPases,
          with UvrA having two ATP binding sites, which have the
          characteristic signature of the family of ABC proteins,
          and UvrB having one ATP binding site that is
          structurally related to that of helicases..
          Length = 176

 Score = 28.7 bits (64), Expect = 2.7
 Identities = 10/30 (33%), Positives = 14/30 (46%)

Query: 64 FPKGRIVEIYGPESSGKTTLALHTIAQSQK 93
           P   +V + G   SGK+TL    +  S K
Sbjct: 18 IPLNVLVVVTGVSGSGKSTLVNEGLYASGK 47


>gnl|CDD|31319 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
          [Inorganic ion transport and metabolism].
          Length = 235

 Score = 28.3 bits (63), Expect = 3.1
 Identities = 10/24 (41%), Positives = 12/24 (50%)

Query: 63 GFPKGRIVEIYGPESSGKTTLALH 86
             KG  V + GP  SGK+TL   
Sbjct: 26 EIEKGERVLLIGPNGSGKSTLLKL 49


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

 Score = 28.2 bits (63), Expect = 3.4
 Identities = 24/91 (26%), Positives = 37/91 (40%), Gaps = 27/91 (29%)

Query: 72  IYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHALDSIYARKLGVDLKNLLISQPDTGE 131
           ++GP   GKTTLA                         I A +LGV+LK   I+     E
Sbjct: 57  LFGPPGLGKTTLA------------------------HIIANELGVNLK---ITSGPALE 89

Query: 132 QALEITDMLVRSGAVDIIVIDSVAALTPRAE 162
           +  ++  +L      D++ ID +  L+P  E
Sbjct: 90  KPGDLAAILTNLEEGDVLFIDEIHRLSPAVE 120


>gnl|CDD|30197 cd02024, NRK1, Nicotinamide riboside kinase (NRK) is an enzyme
          involved in the metabolism of nicotinamide adenine
          dinucleotide (NAD+). This enzyme catalyzes the
          phosphorylation of nicotinamide riboside (NR) to form
          nicotinamide mononucleotide (NMN). It defines the NR
          salvage pathway of NAD+ biosynthesis in addition to the
          pathways through nicotinic acid mononucleotide (NaMN).
          This enzyme can also phosphorylate the anticancer drug
          tiazofurin, which is an analog of nicotinamide
          riboside..
          Length = 187

 Score = 28.3 bits (63), Expect = 3.5
 Identities = 11/20 (55%), Positives = 12/20 (60%)

Query: 69 IVEIYGPESSGKTTLALHTI 88
          IV I G  +SGKTTLA    
Sbjct: 1  IVGISGVTNSGKTTLAKLLQ 20


>gnl|CDD|33254 COG3451, VirB4, Type IV secretory pathway, VirB4 components
           [Intracellular trafficking and secretion].
          Length = 796

 Score = 28.4 bits (63), Expect = 3.5
 Identities = 11/30 (36%), Positives = 14/30 (46%)

Query: 72  IYGPESSGKTTLALHTIAQSQKTGGTCAFV 101
           I GP  +GKT L    +AQ+ K G      
Sbjct: 441 IIGPTGAGKTVLLSFLLAQALKYGNPQIVA 470


>gnl|CDD|33684 COG3896, COG3896, Chloramphenicol 3-O-phosphotransferase [Defense
          mechanisms].
          Length = 205

 Score = 28.1 bits (62), Expect = 3.6
 Identities = 12/23 (52%), Positives = 18/23 (78%)

Query: 63 GFPKGRIVEIYGPESSGKTTLAL 85
          G P+GRIV + G  S+GK+++AL
Sbjct: 19 GMPEGRIVLLNGGSSAGKSSIAL 41


>gnl|CDD|73019 cd03260, ABC_PstB_phosphate_transporter, Phosphate uptake is of
          fundamental importance in the cell physiology of
          bacteria because phosphate is required as a nutrient.
          The Pst system of E. coli comprises four distinct
          subunits encoded by the pstS, pstA, pstB, and pstC
          genes.  The PstS protein is a phosphate-binding protein
          located in the periplasmic space. P stA and PstC are
          hydrophobic and they form the transmembrane portion of
          the Pst system.  PstB is the catalytic subunit, which
          couples the energy of ATP hydrolysis to the import of
          phosphate across cellular membranes through the Pst
          system, often referred as ABC-protein.  PstB belongs to
          one of the largest superfamilies of proteins
          characterized by a highly conserved adenosine
          triphosphate (ATP) binding cassette (ABC), which is
          also a nucleotide binding domain (NBD)..
          Length = 227

 Score = 28.2 bits (63), Expect = 3.7
 Identities = 14/28 (50%), Positives = 17/28 (60%), Gaps = 3/28 (10%)

Query: 56 DIALGIGGFPKGRIVEIYGPESSGKTTL 83
          DI+L I   PKG I  + GP   GK+TL
Sbjct: 18 DISLDI---PKGEITALIGPSGCGKSTL 42


>gnl|CDD|144180 pfam00488, MutS_V, MutS domain V.  This domain is found in proteins
           of the MutS family (DNA mismatch repair proteins) and is
           found associated with pfam01624, pfam05188, pfam05192
           and pfam05190. The mutS family of proteins is named
           after the Salmonella typhimurium MutS protein involved
           in mismatch repair; other members of the family included
           the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have
           various roles in DNA repair and recombination. Human MSH
           has been implicated in non-polyposis colorectal
           carcinoma (HNPCC) and is a mismatch binding protein. The
           aligned region corresponds with domain V of Thermus
           aquaticus MutS, which contains a Walker A motif, and is
           structurally similar to the ATPase domain of ABC
           transporters.
          Length = 234

 Score = 28.3 bits (64), Expect = 3.8
 Identities = 22/57 (38%), Positives = 27/57 (47%), Gaps = 15/57 (26%)

Query: 66  KGRIVEIYGPESSGKTTL----ALHTI-AQSQKTGGTCAFVDAEHAL----DSIYAR 113
           + RI+ I GP   GK+T     AL  I AQ    G   +FV AE A     D I+ R
Sbjct: 41  RSRILLITGPNMGGKSTYLRQVALIVIMAQ---IG---SFVPAESARIGIVDRIFTR 91


>gnl|CDD|31318 COG1121, ZnuC, ABC-type Mn/Zn transport systems, ATPase component
          [Inorganic ion transport and metabolism].
          Length = 254

 Score = 28.3 bits (63), Expect = 3.9
 Identities = 9/20 (45%), Positives = 12/20 (60%)

Query: 64 FPKGRIVEIYGPESSGKTTL 83
            KG I  + GP  +GK+TL
Sbjct: 27 VEKGEITALIGPNGAGKSTL 46


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

 Score = 28.1 bits (62), Expect = 4.0
 Identities = 16/36 (44%), Positives = 21/36 (58%), Gaps = 1/36 (2%)

Query: 55  LDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQ 90
           LD+ L     P  +I+ + GP   GKTTLA H IA+
Sbjct: 314 LDMELDPSKRPPKKILLLCGPPGLGKTTLA-HVIAK 348


>gnl|CDD|72988 cd03229, ABC_Class3, This class is comprised of all BPD (Binding
           Protein Dependent) systems that are largely represented
           in archaea and eubacteria and are primarily involved in
           scavenging solutes from the environment.  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 = 178

 Score = 28.2 bits (63), Expect = 4.1
 Identities = 15/53 (28%), Positives = 21/53 (39%), Gaps = 2/53 (3%)

Query: 64  FPKGRIVEIYGPESSGKTTLALHTIAQSQK-TGGTCAFVDAEHALDSIYARKL 115
              G IV + GP  SGK+TL L  IA  ++   G+      +          L
Sbjct: 23  IEAGEIVALLGPSGSGKSTL-LRCIAGLEEPDSGSILIDGEDLTDLEDELPPL 74


>gnl|CDD|73016 cd03257, ABC_NikE_OppD_transporters, The ABC transporter subfamily
           specific for the transport of dipeptides, oligopeptides
           (OppD), and nickel (NikDE).  The NikABCDE system of E.
           coli belongs to this family and is composed of the
           periplasmic binding protein NikA, two integral membrane
           components (NikB and NikC), and two ATPase (NikD and
           NikE).  The NikABCDE transporter is synthesized under
           anaerobic conditions to meet the increased demand for
           nickel resulting from hydrogenase synthesis.  The
           molecular mechanism of nickel uptake in many bacteria
           and most archaea is not known.  Many other members of
           this ABC family are also involved in the uptake of
           dipeptides and oligopeptides.  The oligopeptide
           transport system (Opp) is a five-component ABC transport
           composed of a membrane-anchored substrate binding
           proteins (SRP), OppA, two transmembrane proteins, OppB
           and OppC, and two ATP-binding domains, OppD and OppF..
          Length = 228

 Score = 27.8 bits (62), Expect = 4.3
 Identities = 24/107 (22%), Positives = 38/107 (35%), Gaps = 26/107 (24%)

Query: 65  PKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHALDSIYARKLGVDLKNLLI 124
            KG  + + G   SGK+TLA   +   + T G+  F               G DL  L  
Sbjct: 29  KKGETLGLVGESGSGKSTLARAILGLLKPTSGSIIF--------------DGKDLLKLSR 74

Query: 125 SQPDTGEQALEITDMLVRSGAVDIIVIDSVAALTPRAEIEGDMGESL 171
                           +R   + ++  D +++L PR  I   + E L
Sbjct: 75  RL------------RKIRRKEIQMVFQDPMSSLNPRMTIGEQIAEPL 109


>gnl|CDD|72976 cd03217, ABC_FeS_Assembly, ABC-type transport system involved in
          Fe-S cluster assembly, ATPase component.  Biosynthesis
          of iron-sulfur clusters (Fe-S) depends on multiprotein
          systems.  The SUF system of E. coli and Erwinia
          chrysanthemi is important for Fe-S biogenesis under
          stressful conditions.  The SUF system is made of six
          proteins: SufC is an atypical cytoplasmic ABC-ATPase,
          which forms a complex with SufB and SufD; SufA plays
          the role of a scaffold protein for assembly of
          iron-sulfur clusters and delivery to target proteins;
          SufS is a cysteine desulfurase which mobilizes the
          sulfur atom from cysteine and provides it to the
          cluster; SufE has no associated function yet..
          Length = 200

 Score = 27.7 bits (62), Expect = 4.4
 Identities = 12/26 (46%), Positives = 15/26 (57%), Gaps = 1/26 (3%)

Query: 64 FPKGRIVEIYGPESSGKTTLALHTIA 89
            KG +  + GP  SGK+TLA  TI 
Sbjct: 23 IKKGEVHALMGPNGSGKSTLA-KTIM 47


>gnl|CDD|31323 COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase
          component [Amino acid transport and metabolism].
          Length = 240

 Score = 27.8 bits (62), Expect = 4.5
 Identities = 11/20 (55%), Positives = 13/20 (65%)

Query: 64 FPKGRIVEIYGPESSGKTTL 83
            KG +V I GP  SGK+TL
Sbjct: 25 VEKGEVVVIIGPSGSGKSTL 44


>gnl|CDD|30653 COG0305, DnaB, Replicative DNA helicase [DNA replication,
           recombination, and repair].
          Length = 435

 Score = 27.9 bits (62), Expect = 4.5
 Identities = 17/84 (20%), Positives = 30/84 (35%), Gaps = 15/84 (17%)

Query: 2   DYRKEMNIVDKSKALEAALSQIQRVYGKGAIMQLGSQGSIFEGIEVVSSGSLGLDIALGI 61
           + +   + V     L+  + +I+  +                G+  V +G   LD     
Sbjct: 146 ERKNSEDFVHIGDLLKETMDEIEARFE-------------NGGLIGVPTGFTDLDEI--T 190

Query: 62  GGFPKGRIVEIYGPESSGKTTLAL 85
            GF  G ++ +      GKT LAL
Sbjct: 191 SGFRPGDLIIVAARPGMGKTALAL 214


>gnl|CDD|32921 COG3107, LppC, Putative lipoprotein [General function prediction
           only].
          Length = 604

 Score = 27.7 bits (61), Expect = 5.0
 Identities = 28/181 (15%), Positives = 59/181 (32%), Gaps = 8/181 (4%)

Query: 57  IALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFV-----DAEHALDSIY 111
               +G   K  +  +          LAL+    S+     C F      +A  A + ++
Sbjct: 320 ADFVVGPLLKPNVEALLASNQQPIPVLALNQPENSRNPAQLCYFALSPEDEARDAANHLW 379

Query: 112 ARKLGVDLKNLLISQPDTGEQALE-ITDMLVRSGAVDIIVIDSVAALTPRAEIEGDMGES 170
            +  G     +L+ + D G++          + G   ++     +    R  I    G  
Sbjct: 380 DQ--GKRNPLVLVPRNDLGDRVANAFNQEWQKLGGGTVLQQKFGSTSELRQGINDGAGIR 437

Query: 171 LPGMQARLMSQALRKLTSSISRSKCILVFINQMRMKIGVMFGSPETTTGGNALKFYSSVR 230
           L G+ A L +    +      +     V+I     ++ ++        G ++   Y+S R
Sbjct: 438 LTGLPADLTTTNGLQTPPLDDQDTIDAVYIVATPSELALIKPMIAMANGSDSPPLYASSR 497

Query: 231 L 231
            
Sbjct: 498 S 498


>gnl|CDD|34357 COG4742, COG4742, Predicted transcriptional regulator
           [Transcription].
          Length = 260

 Score = 27.8 bits (62), Expect = 5.1
 Identities = 16/103 (15%), Positives = 44/103 (42%), Gaps = 10/103 (9%)

Query: 233 IRRVGSIKDKDSITGNQTRV-----KVVKNKMASPFKQVEFDIMYGEGISFFGELIDLGV 287
           ++R+G + D + +  +   +     + ++N  +S          +    S + EL + G+
Sbjct: 106 LKRIGELGDCELLEPDLDHLFEPPPEFLENLSSSKRIMGFSSYFHPSYPSLYLELAEKGI 165

Query: 288 KASIVDKSGAWFSFKGQRLGQGRE-----NSKIFLRENIEIAE 325
             S++     +   K     + +E     N+K+++ + I++A 
Sbjct: 166 DVSLILTEPVFERLKSDYKEELKEFLKLENTKLYVCDGIKLAS 208


>gnl|CDD|31624 COG1435, Tdk, Thymidine kinase [Nucleotide transport and
           metabolism].
          Length = 201

 Score = 27.9 bits (62), Expect = 5.2
 Identities = 20/101 (19%), Positives = 33/101 (32%), Gaps = 8/101 (7%)

Query: 64  FPKGRIVEIYGPESSGKTTLALHTI----AQSQKTGGTCAFVDAEHALDSIYARKLGVDL 119
              G +  IYGP  SGKT   L           K       +D  + +  + +R  G+  
Sbjct: 1   KKMGWLEFIYGPMFSGKTEELLRRARRYKEAGMKVLVFKPAIDTRYGVGKVSSRI-GLSS 59

Query: 120 KNLLISQPDTGEQALEITDMLVRSGAVDIIVIDSVAALTPR 160
           + ++I          +    L     VD ++ID        
Sbjct: 60  EAVVIPSD---TDIFDEIAALHEKPPVDCVLIDEAQFFDEE 97


>gnl|CDD|72987 cd03228, ABCC_MRP_Like, The MRP (Mutidrug Resistance
          Protein)-like transporters are involved in drug,
          peptide, and lipid export.  They belong to the
          subfamily C of the ATP-binding cassette (ABC)
          superfamily of transport proteins.  The ABCC subfamily
          contains transporters with a diverse functional
          spectrum that includes ion transport, cell surface
          receptor, and toxin secretion activities.  The MRP-like
          family, simlar to all ABC proteins, have a common
          four-domain core structure constituted by two
          membrane-spanning domains, each composed of six
          transmembrane (TM) helices, and two nucleotide-binding
          domains (NBD).  ABC transporters are a subset of
          nucleotide hydrolases that contain a signature motif,
          Q-loop, and H-loop/switch region, in addition to, the
          Walker A motif/P-loop and Walker B motif commonly found
          in a number of ATP- and GTP-binding and hydrolyzing
          proteins..
          Length = 171

 Score = 27.7 bits (62), Expect = 5.5
 Identities = 10/21 (47%), Positives = 11/21 (52%)

Query: 64 FPKGRIVEIYGPESSGKTTLA 84
             G  V I GP  SGK+TL 
Sbjct: 25 IKPGEKVAIVGPSGSGKSTLL 45


>gnl|CDD|73057 cd03298, ABC_ThiQ_thiamine_transporter, ABC-type thiamine
          tranport system; part of the binding-protein-dependent
          transport system tbpA-thiPQ for thiamine and TPP.
          Probably responsible for the translocation of thiamine
          across the membrane. 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 = 211

 Score = 27.6 bits (61), Expect = 5.6
 Identities = 14/26 (53%), Positives = 17/26 (65%), Gaps = 1/26 (3%)

Query: 64 FPKGRIVEIYGPESSGKTTLALHTIA 89
          F +G I  I GP  SGK+TL L+ IA
Sbjct: 21 FAQGEITAIVGPSGSGKSTL-LNLIA 45


>gnl|CDD|31949 COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis
           protein [Coenzyme metabolism].
          Length = 161

 Score = 27.6 bits (61), Expect = 5.8
 Identities = 13/38 (34%), Positives = 20/38 (52%)

Query: 68  RIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEH 105
           +I+ I G ++SGKTTL    + + +  G   A V   H
Sbjct: 3   KILGIVGYKNSGKTTLIEKLVRKLKARGYRVATVKHAH 40


>gnl|CDD|30917 COG0572, Udk, Uridine kinase [Nucleotide transport and
          metabolism].
          Length = 218

 Score = 27.5 bits (61), Expect = 6.6
 Identities = 11/26 (42%), Positives = 13/26 (50%)

Query: 65 PKGRIVEIYGPESSGKTTLALHTIAQ 90
           K  I+ I G   SGKTT+A     Q
Sbjct: 6  EKVIIIGIAGGSGSGKTTVAKELSEQ 31


>gnl|CDD|37252 KOG2041, KOG2041, KOG2041, WD40 repeat protein [General function
           prediction only].
          Length = 1189

 Score = 27.3 bits (60), Expect = 6.6
 Identities = 12/46 (26%), Positives = 22/46 (47%)

Query: 102 DAEHALDSIYARKLGVDLKNLLISQPDTGEQALEITDMLVRSGAVD 147
           D E+ ++ +Y  +L  +L+ L  + P+  E    + DM    G  D
Sbjct: 824 DTENQIECLYRLELFGELEVLARTLPEDSELLPVMADMFTSVGMCD 869


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

 Score = 27.2 bits (60), Expect = 6.7
 Identities = 22/79 (27%), Positives = 33/79 (41%), Gaps = 7/79 (8%)

Query: 13  SKALEAALSQIQRVYGKGAIMQLGSQGSIFEGIE---VVSSGSLGLDIALG-IGGF---P 65
            K +   L +++ +  KG    +G      E +E   + S   +GL+  L  +       
Sbjct: 118 GKRVSKVLREVESLGSKGVFEVVGESLDPREKVETRPIQSESDVGLETMLEKLWNRLMED 177

Query: 66  KGRIVEIYGPESSGKTTLA 84
              IV IYG    GKTTLA
Sbjct: 178 DVGIVGIYGMGGVGKTTLA 196


>gnl|CDD|145708 pfam02698, DUF218, DUF218 domain.  This large family of proteins
           contains several highly conserved charged amino acids,
           suggesting this may be an enzymatic domain (Bateman A
           pers. obs). The family includes SanA, which is involved
           in Vancomycin resistance. This protein may be involved
           in murein synthesis.
          Length = 148

 Score = 27.3 bits (61), Expect = 6.9
 Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 3/53 (5%)

Query: 111 YARKLGVDLKNLLI-SQP-DTGEQALEITDMLVRSGAVDIIVIDSVAALTPRA 161
           Y  +LGV  + +L+  Q  +T E A    ++L   G   ++++ S A    RA
Sbjct: 55  YLVELGVPAEAILLEPQSRNTYENARFSAELLRERGLRRVLLVTS-AFHMRRA 106


>gnl|CDD|72975 cd03216, ABC_Carb_Monos_I, This family represents the domain I of
           the carbohydrate uptake proteins that transport only
           monosaccharides (Monos).  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..
          Length = 163

 Score = 27.3 bits (61), Expect = 6.9
 Identities = 26/100 (26%), Positives = 42/100 (42%), Gaps = 9/100 (9%)

Query: 64  FPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHALDSIY-ARKLGVDLKNL 122
             +G +  + G   +GK+TL        +   G       E +  S   AR+ G+     
Sbjct: 23  VRRGEVHALLGENGAGKSTLMKILSGLYKPDSGEILVDGKEVSFASPRDARRAGIA---- 78

Query: 123 LISQPDTGE-QALEITDMLVRSGAVDIIVID-SVAALTPR 160
           ++ Q   GE Q +EI   L R     ++++D   AALTP 
Sbjct: 79  MVYQLSVGERQMVEIARALAR--NARLLILDEPTAALTPA 116


>gnl|CDD|31683 COG1494, GlpX, Fructose-1,6-bisphosphatase/sedoheptulose
           1,7-bisphosphatase and related proteins [Carbohydrate
           transport and metabolism].
          Length = 332

 Score = 27.1 bits (60), Expect = 7.2
 Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 23  IQRVYGKGAIMQLGSQGSIFEGIEVVSSGSLGLDIALGIGGFPKGRI 69
           I  +   GA ++L   G +   I      + G+D+  GIGG P+G I
Sbjct: 171 IAEIRAAGARVRLIPDGDVAAAILTCFPDT-GVDLLYGIGGAPEGVI 216


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

 Score = 27.2 bits (60), Expect = 7.6
 Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 3/35 (8%)

Query: 67  GRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFV 101
           GR V + GP  +GKT LAL   A SQ+ G    F 
Sbjct: 64  GRAVLLAGPPGTGKTALAL---AISQELGPKVPFC 95


>gnl|CDD|31324 COG1127, Ttg2A, ABC-type transport system involved in resistance
          to organic solvents, ATPase component [Secondary
          metabolites biosynthesis, transport, and catabolism].
          Length = 263

 Score = 27.1 bits (60), Expect = 7.7
 Identities = 10/19 (52%), Positives = 13/19 (68%)

Query: 65 PKGRIVEIYGPESSGKTTL 83
          P+G I+ I G   SGK+TL
Sbjct: 32 PRGEILAILGGSGSGKSTL 50


>gnl|CDD|35871 KOG0652, KOG0652, KOG0652, 26S proteasome regulatory complex,
           ATPase RPT5 [Posttranslational modification, protein
           turnover, chaperones].
          Length = 424

 Score = 26.9 bits (59), Expect = 8.0
 Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 2/30 (6%)

Query: 65  PKGRIVEIYGPESSGKTTLALHTIAQSQKT 94
           PKG  V +YGP  +GKT +A    AQ+  T
Sbjct: 205 PKG--VLMYGPPGTGKTLMARACAAQTNAT 232


>gnl|CDD|35402 KOG0181, KOG0181, KOG0181, 20S proteasome, regulatory subunit alpha
           type PSMA2/PRE8 [Posttranslational modification, protein
           turnover, chaperones].
          Length = 233

 Score = 26.8 bits (59), Expect = 8.9
 Identities = 14/40 (35%), Positives = 25/40 (62%), Gaps = 4/40 (10%)

Query: 292 VDKSGAWFSFKGQRLGQGRENSKIFLR----ENIEIAENI 327
           VD SG++F++K   +G+   N+K FL     E++E+ + I
Sbjct: 149 VDPSGSYFAWKATAMGKNYVNAKTFLEKRYNEDLELDDAI 188


>gnl|CDD|33631 COG3839, MalK, ABC-type sugar transport systems, ATPase
          components [Carbohydrate transport and metabolism].
          Length = 338

 Score = 26.8 bits (59), Expect = 9.6
 Identities = 11/26 (42%), Positives = 13/26 (50%), Gaps = 1/26 (3%)

Query: 64 FPKGRIVEIYGPESSGKTTLALHTIA 89
             G  V + GP   GK+TL L  IA
Sbjct: 26 IEDGEFVVLLGPSGCGKSTL-LRMIA 50


>gnl|CDD|35284 KOG0061, KOG0061, KOG0061, Transporter, ABC superfamily (Breast
          cancer resistance protein) [Secondary metabolites
          biosynthesis, transport and catabolism].
          Length = 613

 Score = 26.9 bits (59), Expect = 9.7
 Identities = 11/22 (50%), Positives = 13/22 (59%)

Query: 62 GGFPKGRIVEIYGPESSGKTTL 83
          G    G ++ I GP  SGKTTL
Sbjct: 51 GTAKPGELLAIMGPSGSGKTTL 72


>gnl|CDD|34235 COG4604, CeuD, ABC-type enterochelin transport system, ATPase
          component [Inorganic ion transport and metabolism].
          Length = 252

 Score = 26.7 bits (59), Expect = 9.9
 Identities = 11/20 (55%), Positives = 13/20 (65%)

Query: 64 FPKGRIVEIYGPESSGKTTL 83
           PKG I  I GP  +GK+TL
Sbjct: 24 IPKGGITSIIGPNGAGKSTL 43


>gnl|CDD|73052 cd03293, ABC_NrtD_SsuB_transporters, NrtD and SsuB are the
          ATP-binding subunits of the bacterial ABC-type nitrate
          and sulfonate transport systems, respectively.  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 = 220

 Score = 26.6 bits (59), Expect = 9.9
 Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 4/34 (11%)

Query: 56 DIALGIGGFPKGRIVEIYGPESSGKTTLALHTIA 89
          DI+L +    +G  V + GP   GK+TL L  IA
Sbjct: 22 DISLSV---EEGEFVALVGPSGCGKSTL-LRIIA 51


  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
   0.316    0.134    0.365 

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: 3,993,359
Number of extensions: 208520
Number of successful extensions: 871
Number of sequences better than 10.0: 1
Number of HSP's gapped: 847
Number of HSP's successfully gapped: 155
Length of query: 363
Length of database: 6,263,737
Length adjustment: 95
Effective length of query: 268
Effective length of database: 4,210,882
Effective search space: 1128516376
Effective search space used: 1128516376
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (25.9 bits)