RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|255764514|ref|YP_003065586.2| DNA repair protein RecN
[Candidatus Liberibacter asiaticus str. psy62]
         (554 letters)



>gnl|CDD|30843 COG0497, RecN, ATPase involved in DNA repair [DNA replication,
           recombination, and repair].
          Length = 557

 Score =  502 bits (1295), Expect = e-143
 Identities = 225/556 (40%), Positives = 343/556 (61%), Gaps = 8/556 (1%)

Query: 1   MTRLSIYNIVLIESLDIDFSAGLSILSGDTGSGKSILLDALILVTGGRGDGGLVRRHAEK 60
           +  LSI N  +IE L+++F  GL++L+G+TG+GKSI++DAL L+ GGR D  LVR  A++
Sbjct: 2   LLELSIKNFAIIEELELEFEKGLTVLTGETGAGKSIIIDALGLLLGGRADASLVRHGAKR 61

Query: 61  GQVVAVFEISHLPALEILFAEANLTLEKHVILRRVQFPDGRTKAYVNDQVVSVNFMRAVG 120
            +V A+F++ + PA   L  E  +  ++ VILRRV   DGR++A++N Q VS+  ++ +G
Sbjct: 62  AEVEAIFDLDNPPARAWL-EENGIEDDEEVILRRVISADGRSRAFINGQPVSLAQLKELG 120

Query: 121 SLLIEIHSQHADRSLLDVQGHRKILDSYADI-DLSLCELGTLYRHWCCTADALKKYQEQK 179
            LLI+IH QH  +SLL  +  R++LD++A + +L+       Y+ W      L+  QE++
Sbjct: 121 QLLIDIHGQHEHQSLLKPELQRQLLDAFAGLEELAQEAYQEAYQAWKQARRELEDLQEKE 180

Query: 180 SS-SQDVEFLRFSIDELQALAVQPGEENELVVMRSKILKQERIAVELSSIMDDFHKSSSP 238
              +Q  + L+F ++EL+ L +QPGE+ EL   R ++   E++A  + + ++        
Sbjct: 181 RERAQRADLLQFQLEELEELNLQPGEDEELEEERKRLSNSEKLAEAIQNALELLSGEDDT 240

Query: 239 ISVISSMLRRLER--KSTEVPDLLQKSISFLNEAQENLSDAQHEIERSFSEIQYDAQELA 296
           +S +S + R LE     +E    L +    L EA   L +A  E+     E+++D   L 
Sbjct: 241 VSALSLLGRALEALEDLSEYDGKLSELAELLEEALYELEEASEELRAYLDELEFDPNRLE 300

Query: 297 NIEERLFALRAMSRKYSVSIDQLPELAKKMEEDLADISEGNEKVVSLERVLYEARQAYDR 356
            +EERLFAL++++RKY V+I+ L E   K++E+LA +    E + +LE+ + + +     
Sbjct: 301 EVEERLFALKSLARKYGVTIEDLLEYLDKIKEELAQLDNSEESLEALEKEVKKLKAELLE 360

Query: 357 VAQDISTKRYQFAKMLEKNVMAEMPALKLENVCFTVNITSDKEDISPDGIDRVEFYVQTN 416
            A+ +S  R + AK LEK V AE+ AL +E   FTV +   +E  + DG D+VEF + TN
Sbjct: 361 AAEALSAIRKKAAKELEKEVTAELKALAMEKARFTVELKPLEESPTADGADKVEFLISTN 420

Query: 417 RGENPGPLMKLASGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIGGAVADAIGYRLKQ 476
            GE   PL K+ASGGELSR +LALK++L  +   PTL+FDEVD+GI G VA A+G +L++
Sbjct: 421 PGEPLKPLAKVASGGELSRIMLALKVILSRKDDTPTLIFDEVDTGISGRVAQAVGKKLRR 480

Query: 477 LSKKIQLLAVTHAPQVAARADRHFLVYKTNKPDDTQRIETYVAVLTPQERREEIARMLAG 536
           LS+  Q+L VTH PQVAA AD HFLV K ++     R E+ V  L  +ER EEIARML G
Sbjct: 481 LSEHHQVLCVTHLPQVAAMADTHFLVEKESE---DGRTESRVRPLDKEERVEEIARMLGG 537

Query: 537 SHITEEARAAAEILLE 552
           S +T+EA A A+ LL 
Sbjct: 538 SEVTDEALAHAKELLA 553


>gnl|CDD|73000 cd03241, ABC_RecN, RecN ATPase involved in DNA repair; 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 including sugars, ions, peptides, and more
           complex organic molecules.  The nucleotide binding
           domain shows the highest similarity between all members
           of the family.  ABC transporters are a subset of
           nucleotide hydrolases that contain a signature motif,
           Q-loop, and H-loop/switch region, in addition to, the
           Walker A motif/P-loop and Walker B motif commonly found
           in a number of ATP- and GTP-binding and hydrolyzing
           proteins..
          Length = 276

 Score =  170 bits (432), Expect = 1e-42
 Identities = 73/133 (54%), Positives = 92/133 (69%), Gaps = 3/133 (2%)

Query: 404 DGIDRVEFYVQTNRGENPGPLMKLASGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIG 463
            G+D VEF   TN GE   PL K+ASGGELSR +LALK +L  + ++PTL+FDE+D+GI 
Sbjct: 147 GGLDDVEFLFSTNPGEPLKPLAKIASGGELSRLMLALKAILARKDAVPTLIFDEIDTGIS 206

Query: 464 GAVADAIGYRLKQLSKKIQLLAVTHAPQVAARADRHFLVYKTNKPDDTQRIETYVAVLTP 523
           G VA A+G +LK+LS+  Q+L +TH PQVAA AD HFLV K  +     R  T V  L  
Sbjct: 207 GEVAQAVGKKLKELSRSHQVLCITHLPQVAAMADNHFLVEKEVE---GGRTVTKVRELDK 263

Query: 524 QERREEIARMLAG 536
           +ER EEIARML+G
Sbjct: 264 EERVEEIARMLSG 276



 Score =  146 bits (371), Expect = 1e-35
 Identities = 63/150 (42%), Positives = 94/150 (62%)

Query: 1   MTRLSIYNIVLIESLDIDFSAGLSILSGDTGSGKSILLDALILVTGGRGDGGLVRRHAEK 60
           +  LSI N  LIE L++DF  GL++L+G+TG+GKSILLDAL L+ GGR    L+R  AEK
Sbjct: 1   LLELSIKNFALIEELELDFEEGLTVLTGETGAGKSILLDALSLLLGGRASADLIRSGAEK 60

Query: 61  GQVVAVFEISHLPALEILFAEANLTLEKHVILRRVQFPDGRTKAYVNDQVVSVNFMRAVG 120
             V  VF+IS     + L  E  +  +  +I+RR     GR++ ++N Q V++  +R +G
Sbjct: 61  AVVEGVFDISDEEEAKALLLELGIEDDDDLIIRREISRKGRSRYFINGQSVTLKLLRELG 120

Query: 121 SLLIEIHSQHADRSLLDVQGHRKILDSYAD 150
           SLL++IH QH  ++LL+ +    +LD   D
Sbjct: 121 SLLVDIHGQHDHQNLLNPERQLDLLDGGLD 150


>gnl|CDD|31389 COG1196, Smc, Chromosome segregation ATPases [Cell division and
            chromosome partitioning].
          Length = 1163

 Score = 53.9 bits (129), Expect = 1e-07
 Identities = 68/341 (19%), Positives = 129/341 (37%), Gaps = 27/341 (7%)

Query: 194  ELQALAVQPGEENELVVMRSKILKQERIAVELSSIMDDFHKSSSPISVISSMLRRLERKS 253
            E +  A++   E+          + E +  E+  + +   +    +  +   L  L+ + 
Sbjct: 806  ERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEEL 865

Query: 254  TEVPDLLQKSISFLNEAQENLSDAQHEIERSFSEIQYDAQELANIEERLFALRAMSRKYS 313
             E+    ++    L E +E   + + E+    SE+    +E+  + ERL  L A   +  
Sbjct: 866  EELEAEKEELEDELKELEEEKEELEEELRELESELAELKEEIEKLRERLEELEAKLERLE 925

Query: 314  VSIDQLPELAKKMEEDLAD------ISEGNEKVVSLERVLYEARQAYDRVAQDISTKRYQ 367
            V + +L E  ++  ED  +      I    E++ +L  V   A + Y+ V +     + Q
Sbjct: 926  VELPELEEELEEEYEDTLETELEREIERLEEEIEALGPVNLRAIEEYEEVEERYEELKSQ 985

Query: 368  FAKMLE-----KNVMAEMPALKLENVCFTVNITSDK-----EDISPDGIDRVEF------ 411
               + E       V+ E+   K E    T +  ++      +++   G   +E       
Sbjct: 986  REDLEEAKEKLLEVIEELDKEKRERFKETFDKINENFSEIFKELFGGGTAELELTEPDDP 1045

Query: 412  -----YVQTNRGENPGPLMKLASGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIGGAV 466
                  +           + L SGGE S   LAL   +      P  V DEVD+ +  A 
Sbjct: 1046 LTAGIEISARPPGKKLQSLSLLSGGEKSLTALALLFAIQKYRPAPFYVLDEVDAALDDAN 1105

Query: 467  ADAIGYRLKQLSKKIQLLAVTHAPQVAARADRHFLVYKTNK 507
             + +   +K++SK+ Q + +TH       ADR   V    K
Sbjct: 1106 VERVARLIKEMSKETQFIVITHRKGTMEAADRLVGVTMQEK 1146



 Score = 40.0 bits (93), Expect = 0.002
 Identities = 76/387 (19%), Positives = 151/387 (39%), Gaps = 68/387 (17%)

Query: 17  IDFSAGLSILSGDTGSGKSILLDALILVTGG------RGD--------GGLVRRHAEKGQ 62
           I+FS G + + G  GSGKS ++DA+  V G       R          G   R+ A   +
Sbjct: 20  INFSPGFTAIVGPNGSGKSNIVDAIRFVLGEQSAKNLRASKMSDLIFAGSGNRKPANYAE 79

Query: 63  VVAVFEISHLPALEILFAEANLTLEKHVILRRVQFPDGRTKAYVNDQVVSVNFMRAVGSL 122
           V   F+ S             L  E+  + RR+ + DG ++ Y+N + V           
Sbjct: 80  VELTFDNSD--------NTLPLEYEEISVTRRI-YRDGESEYYINGEKVR---------- 120

Query: 123 LIEIHSQHADRSLLDV------QGH------------RKILDSYADIDLSLCELGTLYRH 164
           L +I    AD  +         QG             RK+++  A +     E       
Sbjct: 121 LKDIQDLLADSGIGKESYSIVSQGKVEEIINAKPEERRKLIEEAAGV-SKYKER------ 173

Query: 165 WCCTADALKKYQEQKSSSQDVEFLRFSID-ELQALAVQPGEENELVVMRSKILKQER--I 221
                +A +K +  + + + +E L   ++ +L+ L  Q  +      +++++ + E   +
Sbjct: 174 ---KEEAERKLERTEENLERLEDLLEELEKQLEKLERQAEKAERYQELKAELRELELALL 230

Query: 222 AVELSSIMDDFHKSSSPISVISSMLRRLERKSTEVPDLLQKSISFLNEAQENLSDAQHEI 281
             +L  +  +  +    +S +   L  L+ +  E    +++  S L E +E L + Q E+
Sbjct: 231 LAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEEL 290

Query: 282 ERSFSEIQYDAQELANIEERLFALRAMSRKYSVSIDQLPE----LAKKMEEDLADISEGN 337
                EI+    E++ + ERL  L     +    +++L E    L +++EE    + E  
Sbjct: 291 LELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELE 350

Query: 338 EKVVSLERVLYEARQAYDRVAQDISTK 364
           + +  LE    E  +    + +++   
Sbjct: 351 QLLAELEEAKEELEEKLSALLEELEEL 377


>gnl|CDD|30768 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
           recombination, and repair].
          Length = 908

 Score = 53.1 bits (127), Expect = 2e-07
 Identities = 73/401 (18%), Positives = 151/401 (37%), Gaps = 46/401 (11%)

Query: 3   RLSIYNIVLIESLDID--FSAGLSILSGDTGSGKSILLDALILVTGGRGDGGLVRRHAEK 60
           RL + N    + +DI+  F +G+ ++ G  G+GKS +LDA+     G+          + 
Sbjct: 5   RLRLKNFRSFKDIDIEKLFDSGIFLIVGPNGAGKSSILDAITFALYGKTPRLGAFSLDDL 64

Query: 61  GQVVAVFEISHLPALEILFAEANLTLEKHVILRRVQFPDGRTKAYVNDQVVSVNFMRAVG 120
            +             +    E    +         +F  GR ++  + Q++ V+  R   
Sbjct: 65  IRAGE----------KSASVELEFEVNGKKYRIEREFRRGRGQSTGSLQIIEVDGERIAD 114

Query: 121 S---------LLIEIHSQHADRSLLDVQGH-RKILDS----YADIDLSLCELGTLYRHWC 166
                      L+ +      RS+   QG     L S      +I   L  L    +   
Sbjct: 115 GKKDVNEKIEELLGLDKDTFTRSVYLPQGEFDAFLKSKPKERKEILDELFGLEKYEKLSE 174

Query: 167 CTADALKKYQEQKSS------------SQDVEFLRFSIDELQALAVQPGEENELVVMRSK 214
              + +K+ + +                  +E L   + EL+ L  +  EE E   +  +
Sbjct: 175 LLKEVIKEAKAKIEELEGQLSELLEDIEDLLEALEEELKELKKLE-EIQEEQEEEELEQE 233

Query: 215 ILKQERIAVELSSIMDDFHKSSSPISVISSMLRRLERKSTEVPDLLQKSISFLNEAQENL 274
           I   E    EL    +   +  + +  I S+     +   E    L++ +  L E  E L
Sbjct: 234 IEALEERLAELEEEKERLEELKARLLEIESLELEALKIREEELRELERLLEELEEKIERL 293

Query: 275 SDAQHEIERSFSEIQYDAQELANIEERLFALRAMSRKYSVSIDQLPELAKKMEEDLADIS 334
            + + EIE    E++     L  +EE L  L+++        ++L +L +K+E+  +++ 
Sbjct: 294 EELEREIEELEEELEGLRALLEELEELLEKLKSLE-------ERLEKLEEKLEKLESELE 346

Query: 335 EGNEKVVSLERVLYEARQAYDRVAQDISTKRYQFAKMLEKN 375
           E  E+   L ++L E  +  +   +++  +  +  + L++ 
Sbjct: 347 ELAEEKNELAKLLEERLKELEERLEELEKELEKALERLKQL 387



 Score = 42.0 bits (98), Expect = 5e-04
 Identities = 69/350 (19%), Positives = 139/350 (39%), Gaps = 22/350 (6%)

Query: 173 KKYQEQKSSSQDVEFLRFSIDELQALAVQPGEENELVVMRSKILKQERIAVELSSIMDDF 232
           +  +E +     ++ L+  ++EL+ L  +  E  EL     ++ K+ +   E  S +++ 
Sbjct: 556 QLKEELRQLEDRLQELKELLEELRLLRTRKEELEELRERLKELKKKLKELEERLSQLEEL 615

Query: 233 HKSSSPISVISSMLRRLERKSTEVPDLLQKSISFLNEAQENLSDAQHEIERSFSEIQYDA 292
            +S       + +    E   +E+ + L          Q  L + + ++E   +EI+ + 
Sbjct: 616 LQSLELSEAENELEEAEEELESEL-EKLNLQAELEELLQAALEELEEKVEELEAEIRREL 674

Query: 293 QELANI---EERLFALRAMSRKYSVSIDQLPELAKKMEEDLADISEGNEKVVSLERVLYE 349
           Q + N    EE+L  L  +  +     ++L EL KK+ E    I E   +   LE +  E
Sbjct: 675 QRIENEEQLEEKLEELEQLEEELEQLREELEELLKKLGEIEQLIEELESRKAELEELKKE 734

Query: 350 ARQAYD--RVAQDISTK--RYQFAKMLEKNVMAEMPALKLENV-CFTVNITSDKEDISPD 404
             +      + +++  K  +      + +N++A++ A   E +   ++N    +      
Sbjct: 735 LEKLEKALELLEELREKLGKAGLRADILRNLLAQIEAEANEILSKLSLNRYDLRRLTIRK 794

Query: 405 GIDRVEFYVQTNRGENPGPLMKLASGGELSRFLLALKIVLVDQ----GSIPTLVFDE--- 457
             +     V  + GE      K  SGGE     LAL++ L D       +  L  DE   
Sbjct: 795 DGNGGLVVVVYDGGEVRPI--KTLSGGERFLASLALRLALSDLLQGRARLELLFLDEPFG 852

Query: 458 -VDSGIGGAVADAIGYRLKQLSKKIQLLAVTHAPQVAARADRHFLVYKTN 506
            +D      +A+ +   L       Q++ ++H  ++  RAD    V K  
Sbjct: 853 TLDEERLEKLAEILEELLSDGR---QIIIISHVEELKERADVRIRVKKDG 899



 Score = 35.4 bits (81), Expect = 0.044
 Identities = 37/194 (19%), Positives = 84/194 (43%), Gaps = 10/194 (5%)

Query: 173 KKYQEQKSSSQDVEFLRFSIDELQALAVQPGEENELVVMRSKILKQERIAVELSSIMDDF 232
           ++   +K  ++  E +     EL+ L  +  E  EL     + L+++   +E      + 
Sbjct: 488 EELSREKEEAELREEIEELEKELRELEEELIELLELEEALKEELEEKLEKLENLLEELEE 547

Query: 233 HKSSSPISVISSMLRRLERKSTEVPDLLQK--SISFLNEAQENLSDAQHEIERSFSEIQY 290
            K    +  +   LR+LE +  E+ +LL++   +    E  E L +   E+++   E++ 
Sbjct: 548 LKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEELEELRERLKELKKKLKELE- 606

Query: 291 DAQELANIEERLFALRAMSRKYSVSIDQLPELAKKMEEDLADISEGNEKVVSLERVLYEA 350
             + L+ +EE L +L     +      +L E  +++E +L  ++   E    L+  L E 
Sbjct: 607 --ERLSQLEELLQSLELSEAEN-----ELEEAEEELESELEKLNLQAELEELLQAALEEL 659

Query: 351 RQAYDRVAQDISTK 364
            +  + +  +I  +
Sbjct: 660 EEKVEELEAEIRRE 673


>gnl|CDD|36182 KOG0964, KOG0964, KOG0964, Structural maintenance of chromosome
            protein 3 (sister chromatid cohesion complex Cohesin,
            subunit SMC3) [Cell cycle control, cell division,
            chromosome partitioning].
          Length = 1200

 Score = 48.4 bits (115), Expect = 5e-06
 Identities = 48/224 (21%), Positives = 92/224 (41%), Gaps = 11/224 (4%)

Query: 293  QELANIEERLFALRAMSRKYSVSIDQLPELAKKMEEDLADISEGNEKVVSLERVLYEARQ 352
            ++L    E L     +++K         E  + +++   ++    + ++ L  VL   ++
Sbjct: 956  KKLHRCNEELKGYSNVNKKALDQFVNFSEQRESLKKRQEELDRSKDSILELITVL--DQR 1013

Query: 353  AYDRVAQDISTKRYQFAKMLEKNV---MAEMPALKLENVCFTVNITSDKEDISPDGIDRV 409
             Y+ +       +  F+++  + V    A +   K +N         D +  S +G D V
Sbjct: 1014 KYEAIDLTFKQVKKNFSEVFSRLVPGGTALIIMRKRDNANDHDEDDGDMDGESNEGKDSV 1073

Query: 410  EFY------VQTNRGENPGPLMKLASGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIG 463
            E Y      V  N  +     M+  SGG+ S   LAL   +      P  +FDE+D+ + 
Sbjct: 1074 EMYTGISIKVSFNSKQGETLEMEQLSGGQKSVVALALIFAIQRCDPAPFYLFDEIDAALD 1133

Query: 464  GAVADAIGYRLKQLSKKIQLLAVTHAPQVAARADRHFLVYKTNK 507
                 A+   +K+LS   Q +  T  P++ + AD+ + V   NK
Sbjct: 1134 AQYRTAVADLIKELSDSAQFITTTFRPELLSVADKFYGVKFENK 1177


>gnl|CDD|72986 cd03227, ABC_Class2, ABC-type Class 2 contains systems involved in
           cellular processes other than transport.  These families
           are characterised by the fact that the ABC subunit is
           made up of duplicated, fused ABC modules (ABC2).  No
           known transmembrane proteins or domains are associated
           with these proteins..
          Length = 162

 Score = 47.3 bits (112), Expect = 1e-05
 Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 1/80 (1%)

Query: 428 ASGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIGGAVADAIGYRLKQLSKKI-QLLAV 486
            SGGE     LAL + L      P  + DE+D G+      A+   + +   K  Q++ +
Sbjct: 78  LSGGEKELSALALILALASLKPRPLYILDEIDRGLDPRDGQALAEAILEHLVKGAQVIVI 137

Query: 487 THAPQVAARADRHFLVYKTN 506
           TH P++A  AD+   + K  
Sbjct: 138 THLPELAELADKLIHIKKVI 157



 Score = 42.6 bits (100), Expect = 3e-04
 Identities = 21/55 (38%), Positives = 29/55 (52%), Gaps = 1/55 (1%)

Query: 16 DIDFSAG-LSILSGDTGSGKSILLDALILVTGGRGDGGLVRRHAEKGQVVAVFEI 69
          D+ F  G L+I++G  GSGKS +LDA+ L  GG       R   + G +VA    
Sbjct: 15 DVTFGEGSLTIITGPNGSGKSTILDAIGLALGGAQSATRRRSGVKAGCIVAAVSA 69


>gnl|CDD|73031 cd03272, ABC_SMC3_euk, Eukaryotic SMC3 proteins; SMC proteins are
           large (approximately 110 to 170 kDa), and each is
           arranged into five recognizable domains.  Amino-acid
           sequence homology of SMC proteins between species is
           largely confined to the amino- and carboxy-terminal
           globular domains.  The amino-terminal domain contains a
           'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the
           single-letter amino-acid code), which by mutational
           studies has been shown to be essential in several
           proteins.  The carboxy-terminal domain contains a
           sequence (the DA-box) that resembles a 'Walker B' motif,
           and a motif with homology to the signature sequence of
           the ATP-binding cassette (ABC) family of ATPases.  The
           sequence homology within the carboxy-terminal domain is
           relatively high within the SMC1-SMC4 group, whereas SMC5
           and SMC6 show some divergence in both of these
           sequences.  In eukaryotic cells, the proteins are found
           as heterodimers of SMC1 paired with SMC3, SMC2 with
           SMC4, and SMC5 with SMC6 (formerly known as Rad18)..
          Length = 243

 Score = 46.0 bits (109), Expect = 3e-05
 Identities = 27/93 (29%), Positives = 44/93 (47%)

Query: 415 TNRGENPGPLMKLASGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIGGAVADAIGYRL 474
           TN  ++    M+  SGG+ S   LAL   +      P  +FDE+D+ +      A+   +
Sbjct: 146 TNMKQDEQQEMQQLSGGQKSLVALALIFAIQKCDPAPFYLFDEIDAALDAQYRTAVANMI 205

Query: 475 KQLSKKIQLLAVTHAPQVAARADRHFLVYKTNK 507
           K+LS   Q +  T  P++   AD+ + V   NK
Sbjct: 206 KELSDGAQFITTTFRPELLEVADKFYGVKFRNK 238


>gnl|CDD|73037 cd03278, ABC_SMC_barmotin, Barmotin is a tight junction-associated
           protein expressed in rat epithelial cells which is
           thought to have an important regulatory role in tight
           junction barrier function.  Barmotin belongs to the SMC
           protein family.  SMC proteins are large (approximately
           110 to 170 kDa), and each is arranged into five
           recognizable domains.  Amino-acid sequence homology of
           SMC proteins between species is largely confined to the
           amino- and carboxy-terminal globular domains. The
           amino-terminal domain contains a 'Walker A'
           nucleotide-binding domain (GxxGxGKS/T, in the
           single-letter amino-acid code), which by mutational
           studies has been shown to be essential in several
           proteins.  The carboxy-terminal domain contains a
           sequence (the DA-box) that resembles a 'Walker B' motif,
           and a motif with homology to the signature sequence of
           the ATP-binding cassette (ABC) family of ATPases.  The
           sequence homology within the carboxy-terminal domain is
           relatively high within the SMC1-SMC4 group, whereas SMC5
           and SMC6 show some divergence in both of these
           sequences.  In eukaryotic cells, the proteins are found
           as heterodimers of SMC1 paired with SMC3, SMC2 with
           SMC4, and SMC5 with SMC6 (formerly known as Rad18)..
          Length = 197

 Score = 45.4 bits (108), Expect = 3e-05
 Identities = 25/74 (33%), Positives = 35/74 (47%)

Query: 425 MKLASGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIGGAVADAIGYRLKQLSKKIQLL 484
           + L SGGE +   LAL   +      P  V DEVD+ +  A  +     LK+ SK+ Q +
Sbjct: 111 LSLLSGGEKALTALALLFAIFRVRPSPFCVLDEVDAALDDANVERFARLLKEFSKETQFI 170

Query: 485 AVTHAPQVAARADR 498
            +TH       ADR
Sbjct: 171 VITHRKGTMEAADR 184



 Score = 33.5 bits (77), Expect = 0.16
 Identities = 23/75 (30%), Positives = 31/75 (41%), Gaps = 5/75 (6%)

Query: 13 ESLDIDFSAGLSILSGDTGSGKSILLDALILVTGGRGDGGLVRRHAEKGQVVAVFEISHL 72
          +   I F  GL+ + G  GSGKS ++DA+  V G +    L     EK   V        
Sbjct: 14 DKTTIPFPPGLTAIVGPNGSGKSNIIDAIRWVLGEQSAKSL---RGEKMSDVIFAGSETR 70

Query: 73 PALEILFAEANLTLE 87
                FAE  LT +
Sbjct: 71 KPAN--FAEVTLTFD 83


>gnl|CDD|31388 COG1195, RecF, Recombinational DNA repair ATPase (RecF pathway)
          [DNA replication, recombination, and repair].
          Length = 363

 Score = 44.1 bits (104), Expect = 1e-04
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 5/72 (6%)

Query: 2  TRLSIYNIVLIESLDIDFSAGLSILSGDTGSGKSILLDALILVTGGRG-----DGGLVRR 56
            L + N      LD+D S G+++L G+ G GK+ LL+A+ L+  GR      D  L+R 
Sbjct: 4  LSLLLRNFRNYAELDLDLSPGVNVLVGENGQGKTNLLEAIYLLALGRSHRTSRDKELIRT 63

Query: 57 HAEKGQVVAVFE 68
           A++ ++ A  +
Sbjct: 64 GADEAEISARVQ 75


>gnl|CDD|33731 COG3950, COG3950, Predicted ATP-binding protein involved in
           virulence [General function prediction only].
          Length = 440

 Score = 42.3 bits (99), Expect = 3e-04
 Identities = 53/299 (17%), Positives = 103/299 (34%), Gaps = 28/299 (9%)

Query: 216 LKQERIAVELSSIMDDFHKSSSPISVISSMLRRLERKSTEVPDLLQKSISFLNEAQENLS 275
           L+ + + +EL  I       S+P   ++ +    ++K T V           N+ +E   
Sbjct: 58  LRFKSLKIELDDIELCIMSQSNPTVAVAVVEYENDKKRTWVLTK--------NKNKELDV 109

Query: 276 DAQHEIERSFSEIQY-DAQELAN--IEERLFALRAMSRKYSVSIDQLPELAKKMEEDL-- 330
           D   EI      +   D+  +        L A     R +          AK        
Sbjct: 110 DKVDEILNKLGILMNIDSDPILKSYNHLPLLAYYGTKRLWLHKRKH----AKSDFLRKSN 165

Query: 331 --ADISEGNEKVVSLERVLYEARQAYDRVAQDISTKRYQFAKMLEKNVMAEMPALKLENV 388
             A+ + G    +          + Y+     + +   +  + + +N+ +E  A   + +
Sbjct: 166 PNAERTFGYADCLENTSNFKSFIEWYEHFILQLISPSAEEKEQISQNLDSEFIARLQDAI 225

Query: 389 CFTVNITSDKEDISPDGIDRVEFYVQTNRGENP------GPLMKLASGGELSRFLLALKI 442
              ++ TS  + +         F    N GE P      GP  K A   +++R  + L  
Sbjct: 226 NENISSTSWNDLLIGSQRKHELFMKHGNGGEIPLSELSDGPRTKFALVADIARRCVVLNP 285

Query: 443 VLVDQGSIPT---LVFDEVDSGIGGAVADAIGYRLKQLSKKIQLLAVTHAPQVAARADR 498
            L D  +  T   ++ DE+D  +       I  +L     +IQ +  TH+P V +  + 
Sbjct: 286 YLSDALAKLTPGIVLIDEIDLFLHPKWQQQINQKLLSAFPEIQFIVSTHSPFVLSTVNG 344



 Score = 35.4 bits (81), Expect = 0.044
 Identities = 15/40 (37%), Positives = 24/40 (60%), Gaps = 1/40 (2%)

Query: 3  RLSIYNIVLIESLDIDFSAG-LSILSGDTGSGKSILLDAL 41
          ++S+ N     +LDI F     +I+ G  GSGK+ +LDA+
Sbjct: 5  KISLNNFRCFLNLDITFGESETTIIVGPNGSGKTTVLDAI 44


>gnl|CDD|35383 KOG0161, KOG0161, KOG0161, Myosin class II heavy chain
           [Cytoskeleton].
          Length = 1930

 Score = 42.1 bits (99), Expect = 4e-04
 Identities = 36/141 (25%), Positives = 57/141 (40%), Gaps = 10/141 (7%)

Query: 246 LRRLERKSTEVPDLLQKSISFLNEAQENLSDAQHEIERSFSEIQYDAQELANIEERLFAL 305
           +R  E +  ++ + LQKS S   E +E L     E      ++Q + + LA  EE L  L
Sbjct: 840 MRAKEEEIQKLKEELQKSESKRKELEEKLVKLLEEKNDLQEQLQAEKENLAEAEELLERL 899

Query: 306 RAMSRKYSVSIDQLPELAKKMEEDLADISEGNEKVVSLERVLYEARQAYDRVAQDISTKR 365
           RA          +  EL K+++E    + E  EK   LER   +  Q    + + +    
Sbjct: 900 RA----------EKQELEKELKELKERLEEEEEKNAELERKKRKLEQEVQELKEQLEELE 949

Query: 366 YQFAKMLEKNVMAEMPALKLE 386
               K+  +   AE     LE
Sbjct: 950 LTLQKLELEKNAAENKLKNLE 970



 Score = 33.3 bits (76), Expect = 0.16
 Identities = 40/252 (15%), Positives = 92/252 (36%), Gaps = 33/252 (13%)

Query: 169  ADALKKYQE-QKSSSQDVEFLRFSI-DELQALAVQPGEENELVVMRSKILKQERIAVELS 226
            A   KK++E      +++E L+  +   LQ L  Q    N       K     R+  EL 
Sbjct: 1360 AQWKKKFEEEVLQRLEELEELKKKLQQRLQELEEQIEAANAKNASLEKAKN--RLQQELE 1417

Query: 227  SIMDDFHKSSSPISVISSMLRRLERKSTEVPDLLQKSISFLNEAQENLSDAQHEIERSFS 286
             +  D  +S + ++ +    +R E                L E ++ L   Q E++ +  
Sbjct: 1418 DLQLDLERSRAAVAALEKKQKRFE--------------KLLAEWKKKLEKLQAELDAA-- 1461

Query: 287  EIQYDAQELANIEERLFALRAMSRKYSVSIDQLPELAKKMEEDLADISEGNEKVVSLERV 346
                  +EL  +   L  L+    +    +++L    K + +++ D+ E  +      + 
Sbjct: 1462 -----QRELRQLSTELQKLKNALEELLEQLEELRRENKNLSQEIEDLEEQKD---EGGKR 1513

Query: 347  LYEARQAYDRVAQDISTKRYQFAKMLEKNVMAEMPALKLENVCFTVNITSDKEDISPDGI 406
            ++E  +   R+ Q+    +    ++       E   L+L+     + +   + +I     
Sbjct: 1514 VHELEKEKRRLEQEKEELQAALEELEAALEAEEDKKLRLQ-----LELQQLRSEIERRLQ 1568

Query: 407  DRVEFYVQTNRG 418
            ++ E   +  + 
Sbjct: 1569 EKDEEIEELRKN 1580



 Score = 29.8 bits (67), Expect = 1.9
 Identities = 35/178 (19%), Positives = 68/178 (38%), Gaps = 22/178 (12%)

Query: 178  QKSSSQDVEFLRFSIDELQALAVQPGEENELVVMRSKILKQERIAVELSSIMDDFHKSSS 237
            +K  +  +  L+  +++LQ    +  +E   +      L  E +    S   D       
Sbjct: 1184 RKKHADSLAELQEQLEQLQKDKAKLEKEKSDLQREIADLAAE-LEQLSSEKKD------- 1235

Query: 238  PISVISSMLRRLERKSTEVPDLLQKSISFLNEAQENLSDAQHEIERSFSEIQYDAQELAN 297
                +    ++LE         L +    L+E +   +D   +  R  +E +  +++L  
Sbjct: 1236 ----LEKKDKKLE-------AQLSELQLKLDEQERLRNDLTAKRSRLQNENEELSRQL-- 1282

Query: 298  IEERLFALRAMSRKYSVSIDQLPELAKKMEEDLADISEGNEKVVSLERVLYEARQAYD 355
             EE    L A+SR       QL EL +++EE+  + S     +  LE  L   R+  +
Sbjct: 1283 -EEAEAKLSALSRDKQALESQLEELKRQLEEETREKSALENALRQLEHELDLLREQLE 1339



 Score = 28.3 bits (63), Expect = 5.9
 Identities = 25/142 (17%), Positives = 63/142 (44%), Gaps = 10/142 (7%)

Query: 205  ENELVVMRSKILKQERIAVELSSIMDDFHKSSSPISVISSMLRRLERKSTEVPDLLQKSI 264
            E  L  +R++  + E+   EL   +++  + ++    +    R+LE++  E+ + L++  
Sbjct: 893  EELLERLRAEKQELEKELKELKERLEEEEEKNA---ELERKKRKLEQEVQELKEQLEELE 949

Query: 265  SFLNEAQENLSDAQHEIERSFSEIQYDAQELANIEERLFALRAMSRKYSVSIDQLPELAK 324
              L + +   + A+++++    EI    + ++ + +    L    R+    +    E AK
Sbjct: 950  LTLQKLELEKNAAENKLKNLEEEINSLDENISKLSKEKKELEERIRELQDDLQAEEEKAK 1009

Query: 325  -------KMEEDLADISEGNEK 339
                   K+E+ L D+    E+
Sbjct: 1010 SLNKAKAKLEQQLDDLEVTLER 1031



 Score = 28.3 bits (63), Expect = 6.3
 Identities = 26/138 (18%), Positives = 51/138 (36%), Gaps = 19/138 (13%)

Query: 244  SMLRRLERKSTEVPDLLQKSISFLNEAQENL----SDAQHEIERSFSEIQYDAQELANIE 299
            + +  L +K  +    LQ+ +  L + +  L    SD Q EI    +E++  + E  ++E
Sbjct: 1178 AQIEELRKKHADSLAELQEQLEQLQKDKAKLEKEKSDLQREIADLAAELEQLSSEKKDLE 1237

Query: 300  ERLFALRAMSRKYSVSIDQLPELAKKMEEDLADISEG----NEKVVSLERVLYEARQAYD 355
            +         +K    + +L     + E    D++        +   L R L EA    +
Sbjct: 1238 K-------KDKKLEAQLSELQLKLDEQERLRNDLTAKRSRLQNENEELSRQLEEA----E 1286

Query: 356  RVAQDISTKRYQFAKMLE 373
                 +S  +      LE
Sbjct: 1287 AKLSALSRDKQALESQLE 1304


>gnl|CDD|145545 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain.  This domain is
            found at the N terminus of SMC proteins. The SMC
            (structural maintenance of chromosomes) superfamily
            proteins have ATP-binding domains at the N- and
            C-termini, and two extended coiled-coil domains separated
            by a hinge in the middle. The eukaryotic SMC proteins
            form two kind of heterodimers: the SMC1/SMC3 and the
            SMC2/SMC4 types. These heterodimers constitute an
            essential part of higher order complexes, which are
            involved in chromatin and DNA dynamics. This family also
            includes the RecF and RecN proteins that are involved in
            DNA metabolism and recombination.
          Length = 1162

 Score = 41.9 bits (98), Expect = 5e-04
 Identities = 61/349 (17%), Positives = 110/349 (31%), Gaps = 20/349 (5%)

Query: 169  ADALKKYQEQKSSSQDVEFLRFSIDELQALAVQPGEENELVVMRSKILKQERIAVELSSI 228
             + L   QE+K   +++E L   + E Q L     EE E +       +  +  +     
Sbjct: 820  EEQLLIEQEEKIKEEELEELALELKEEQKLEKLAEEELERLEEEITKEELLQELLLKEEE 879

Query: 229  MDDF---HKSSSPISVISSMLRRLERKSTEVPDLLQKSISFLNEAQENLSDAQHEIERSF 285
            +++     +  S         + LE +S +   L +K         E             
Sbjct: 880  LEEQKLKDELESKEEKEKEEKKELEEESQKDNLLEEKENEIEERIAEEAIILLKYES--E 937

Query: 286  SEIQYDAQELANIEERLFALRAMSRKYSVSIDQLPELAKKMEEDLADISEGNEKVVSLER 345
             E     +     +E         R   +      EL       +A+  E  E+    E 
Sbjct: 938  PEELLLEEADEKEKEEDNKEEEEERNKRLL-LAKEELGNVNLMAIAEFEEKEERYNKDEL 996

Query: 346  VLYEARQAYDRVAQ-DISTKRYQFAKMLEKNVMAEMPALKLENVCFTVNIT----SDKED 400
                  +    + +  I     +F + LE  V       K+               D +D
Sbjct: 997  KKERLEEEKKELLREIIEETCQRFKEFLELFVSINRGLNKVFFYLELGGSAELRLEDSDD 1056

Query: 401  ISPDGIDRVEFYVQTNRGENPGPLMKLASGGELSRFLLALKIVLVDQGSIPT--LVFDEV 458
                GI      +           +   SGGE +  L+AL ++   Q   P    + DE+
Sbjct: 1057 PFSGGI-----EISARPPGKGVKNLDNLSGGEKT--LVALALIFAIQKYRPAPFYLLDEI 1109

Query: 459  DSGIGGAVADAIGYRLKQLSKKIQLLAVTHAPQVAARADRHFLVYKTNK 507
            D+ +       +   LK+LSK  Q + ++   ++  +ADR   VY    
Sbjct: 1110 DAALDDQNVSRVANYLKELSKNAQFIVISLREEMLEKADRLVGVYMVEN 1158



 Score = 34.6 bits (79), Expect = 0.075
 Identities = 28/109 (25%), Positives = 50/109 (45%), Gaps = 10/109 (9%)

Query: 13  ESLDIDFSAGLSILSGDTGSGKSILLDALILVTGGRGDGGLVRRHAEKGQVVAVFEISHL 72
           +++ + FS G + + G  GSGKS +LDA++ V G R    L    +E+   +  +  S  
Sbjct: 15  KTVILPFSPGFTAIVGPNGSGKSNILDAILFVLGERSAKSL---RSERLSDLIHYSKSGA 71

Query: 73  PAL----EILFAE--ANLTLEKH-VILRRVQFPDGRTKAYVNDQVVSVN 114
                   I F      L ++   V +RR  +  G ++ Y+N + V+  
Sbjct: 72  FVNSAEVTITFDNEDKELPIDDPEVSIRRRVYRGGDSEYYINGKDVTKK 120


>gnl|CDD|73035 cd03276, ABC_SMC6_euk, Eukaryotic SMC6 proteins; SMC proteins are
          large (approximately 110 to 170 kDa), and each is
          arranged into five recognizable domains.  Amino-acid
          sequence homology of SMC proteins between species is
          largely confined to the amino- and carboxy-terminal
          globular domains. The amino-terminal domain contains a
          'Walker A' nucleotide-binding domain (GxxGxGKS/T, in
          the single-letter amino-acid code), which by mutational
          studies has been shown to be essential in several
          proteins.  The carboxy-terminal domain contains a
          sequence (the DA-box) that resembles a 'Walker B'
          motif, and a motif with homology to the signature
          sequence of the ATP-binding cassette (ABC) family of
          ATPases.  The sequence homology within the
          carboxy-terminal domain is relatively high within the
          SMC1-SMC4 group, whereas SMC5 and SMC6 show some
          divergence in both of these sequences.  In eukaryotic
          cells, the proteins are found as heterodimers of SMC1
          paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6
          (formerly known as Rad18)..
          Length = 198

 Score = 40.6 bits (95), Expect = 0.001
 Identities = 18/71 (25%), Positives = 35/71 (49%), Gaps = 4/71 (5%)

Query: 3  RLSIYNIVLIESLDIDFSAGLSILSGDTGSGKSILLDALILVTGGRGD----GGLVRRHA 58
           +++ N +    L I+F   ++ + G+ GSGKS +L AL +  GG+      G  ++   
Sbjct: 3  SITLKNFMCHRHLQIEFGPRVNFIVGNNGSGKSAILTALTIGLGGKASDTNRGSSLKDLI 62

Query: 59 EKGQVVAVFEI 69
          + G+  A   +
Sbjct: 63 KDGESSAKITV 73


>gnl|CDD|73001 cd03242, ABC_RecF, RecF is a recombinational DNA repair ATPase
          that maintains replication in the presence of DNA
          damage.  When replication is prematurely disrupted by
          DNA damage, several recF pathway gene products play
          critical roles processing the arrested replication
          fork, allowing it to resume and complete its task.
          This CD represents the nucleotide binding domain of
          RecF.  RecF  belongs to a large superfamily of ABC
          transporters involved in the transport of a wide
          variety of different compounds including sugars, ions,
          peptides, and more complex organic molecules.  The
          nucleotide binding domain shows the highest similarity
          between all members of the family.  ABC transporters
          are a subset of nucleotide hydrolases with 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 = 270

 Score = 40.2 bits (94), Expect = 0.001
 Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 5/83 (6%)

Query: 1  MTRLSIYNIVLIESLDIDFSAGLSILSGDTGSGKSILLDALILVTGGRG-----DGGLVR 55
          +  L + N      L+++F  G+++L G+   GK+ LL+A+ L+  G+      D  L+R
Sbjct: 1  LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAISLLATGKSHRTSRDKELIR 60

Query: 56 RHAEKGQVVAVFEISHLPALEIL 78
            AE+ ++ AV E         L
Sbjct: 61 WGAEEAKISAVLERQGGELALEL 83


>gnl|CDD|31767 COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding
           [General function prediction only].
          Length = 239

 Score = 39.5 bits (92), Expect = 0.002
 Identities = 37/187 (19%), Positives = 76/187 (40%), Gaps = 27/187 (14%)

Query: 228 IMDDFHKSSSPISVISSMLRRLERKSTEVPDLLQKSISFLNEAQENLSDAQHEIERSFSE 287
           +M++  KS   I  +     RLE +  E+   L+K+ + L    + L   + E+E   ++
Sbjct: 1   MMNNNLKSLLAIQKLDLEKDRLEPRIKEIRKALKKAKAELEALNKALEALEIELEDLENQ 60

Query: 288 IQYDAQELANIEERLFALRA---------MSRKYSVSIDQLPELAKKMEEDLAD------ 332
           +     E+  I ER+                R  ++ I    E    +E++LA+      
Sbjct: 61  VSQLESEIQEIRERIKRAEEKLSAVKDERELRALNIEIQIAKERINSLEDELAELMEEIE 120

Query: 333 -----ISEGNEKVVSLERVLYEARQAYD-------RVAQDISTKRYQFAKMLEKNVMAEM 380
                I +  E++  LE+ L EA    +          Q++S+KR +  + L+  +++E 
Sbjct: 121 KLEKEIEDLKERLERLEKNLAEAEARLEEEVAEIREEGQELSSKREELKEKLDPELLSEY 180

Query: 381 PALKLEN 387
             ++   
Sbjct: 181 ERIRKNK 187


>gnl|CDD|72999 cd03240, ABC_Rad50, The catalytic domains of Rad50 are similar to
          the ATP-binding cassette of ABC transporters, but are
          not associated with membrane-spanning domains.  The
          conserved ATP-binding motifs common to Rad50 and the
          ABC transporter family include the Walker A and Walker
          B motifs, the Q loop, a histidine residue in the switch
          region, a D-loop, and a conserved LSGG sequence.  This
          conserved sequence, LSGG, is the most specific and
          characteristic motif of this family and is thus known
          as the ABC signature sequence..
          Length = 204

 Score = 39.4 bits (92), Expect = 0.003
 Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 10/77 (12%)

Query: 2  TRLSIYNIVLI-ESLDIDFSAGLSILSGDTGSGKSILLDALILVT---------GGRGDG 51
           +LSI NI    E  +I+F + L+++ G  G+GK+ +++AL             GG  D 
Sbjct: 2  DKLSIRNIRSFHERSEIEFFSPLTLIVGQNGAGKTTIIEALKYALTGELPPNSKGGAHDP 61

Query: 52 GLVRRHAEKGQVVAVFE 68
           L+R    + QV   FE
Sbjct: 62 KLIREGEVRAQVKLAFE 78



 Score = 29.8 bits (67), Expect = 2.0
 Identities = 26/87 (29%), Positives = 38/87 (43%), Gaps = 13/87 (14%)

Query: 429 SGGELSRFLLALKIVL----VDQGSIPTLVFDE----VDSG-IGGAVADAIGYRLKQLSK 479
           SGGE  + L +L I L        +   L  DE    +D   I  ++A+ I  R  Q  K
Sbjct: 117 SGGE--KVLASLIIRLALAETFGSNCGILALDEPTTNLDEENIEESLAEIIEERKSQ--K 172

Query: 480 KIQLLAVTHAPQVAARADRHFLVYKTN 506
             QL+ +TH  ++   AD  + V K  
Sbjct: 173 NFQLIVITHDEELVDAADHIYRVEKDG 199


>gnl|CDD|34593 COG4988, CydD, ABC-type transport system involved in cytochrome bd
           biosynthesis, ATPase and permease components [Energy
           production and conversion / Posttranslational
           modification, protein turnover, chaperones].
          Length = 559

 Score = 38.3 bits (89), Expect = 0.005
 Identities = 45/175 (25%), Positives = 75/175 (42%), Gaps = 22/175 (12%)

Query: 361 ISTKRYQFAKMLEKNVMAEMPALKLENVCFTVNITSDKEDIS-PDGIDRVEFYVQTNRGE 419
           +S   Y FA  + +N++   P    E +   ++     E +  PDG+D       T  GE
Sbjct: 400 VSQNPYLFAGTIRENILLARPDASDEEIIAALDQAGLLEFVPKPDGLD-------TVIGE 452

Query: 420 NPGPLMKLASGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIGGAVADAIGYRLKQLSK 479
               L    SGG+  R  LAL   L+   S+  L+ DE  + +       I   L++L+K
Sbjct: 453 GGAGL----SGGQAQR--LALARALLSPASL--LLLDEPTAHLDAETEQIILQALQELAK 504

Query: 480 KIQLLAVTHAPQVAARADR-----HFLVYKTNKPDDTQRIETYVA-VLTPQERRE 528
           +  +L +TH  + AA ADR     +  + +    ++    +   A +L  QE R 
Sbjct: 505 QKTVLVITHRLEDAADADRIVVLDNGRLVEQGTHEELSEKQGLYANLLKQQEGRR 559


>gnl|CDD|36214 KOG0996, KOG0996, KOG0996, Structural maintenance of chromosome
            protein 4 (chromosome condensation complex Condensin,
            subunit C) [Chromatin structure and dynamics, Cell cycle
            control, cell division, chromosome partitioning].
          Length = 1293

 Score = 36.5 bits (84), Expect = 0.019
 Identities = 38/222 (17%), Positives = 76/222 (34%), Gaps = 41/222 (18%)

Query: 176  QEQKSSSQDVEFLRFSIDELQALAVQPGEENELVVMRSKILKQERIAVELSSIMDDFHKS 235
            QE+ +    ++ L+  IDE+    VQ  +                         D   K 
Sbjct: 878  QEKAAKKARIKELQNKIDEIGGEKVQAQK-------------------------DKVEKI 912

Query: 236  SSPISVISSMLRRLERKSTEVPDLLQKSISFLNEAQENLSDAQHEIERSFSEIQYDAQEL 295
            +  +  + + + +L          + K       AQ+ LS+ + EIE +  E+    +EL
Sbjct: 913  NEQLDKLEADIAKLTVAIKTSDRNIAK-------AQKKLSELEREIEDTEKELDDLTEEL 965

Query: 296  ANIEERLFALRAMSRKYSVSI----DQLPELAKKMEEDLADISEGNEKVVSLERVLYEAR 351
              +EE+   L    ++   S+     +L +L  ++E      +E   + + +E  L    
Sbjct: 966  KGLEEKAAELEKEYKEAEESLKEIKKELRDLKSELENIKKSENELKAERIDIENKLEAIN 1025

Query: 352  QAYDRVAQDIS-----TKRYQFAKMLEKNVMAEMPALKLENV 388
               + +   I       K+     M E     E+     E +
Sbjct: 1026 GELNEIESKIKQPEKELKKLSLCNMTETRPQIELDVESPEEL 1067



 Score = 29.5 bits (66), Expect = 2.4
 Identities = 65/404 (16%), Positives = 134/404 (33%), Gaps = 67/404 (16%)

Query: 19  FSAGLSILSGDTGSGKSILLDALILVTGGRGD-------GGLVRRHAEKGQVVAVFEISH 71
           F    + + G  GSGKS ++D+++ V G R           L+ +      + +     H
Sbjct: 106 FHKSFTAIVGPNGSGKSNVIDSMLFVFGFRASKIRSKKLSALIHKSDGHPNLQSCSVEVH 165

Query: 72  LPALEILFAEANLTL-EKHVILRRVQFPDGRTKAYVNDQVVSVNFMRAVGSLLIEIHSQH 130
              +          + +    + R  F D  +K Y+N +  S      V  LL       
Sbjct: 166 FQKIIDKPGGTYEVVPDSEFTITRTAFRDNSSKYYINGKEASFK---DVTKLLKSHGIDL 222

Query: 131 ADRSLLDVQG---------------HRKILDSY-----------ADIDLSLCELGTLYRH 164
                L +QG               + + +  Y             I+  +  +  L   
Sbjct: 223 EHNRFLILQGEVEQIAMMKPKAQTENDEGMLEYLEDIIGTNRYKEPIEELMRRVERLNED 282

Query: 165 WCCTADALKKYQEQKSSSQD--VEFLRFSIDELQALAVQP-GEENELVVMRSKILKQ--- 218
                + +K  +++K + +    E L F   E +    +    +  L   R+KI +    
Sbjct: 283 RSEKENRVKLVEKEKKALEGPKNEALEFLKKENELFRKKNKLCQYILYESRAKIAEMQEE 342

Query: 219 -ERIAVELSSIMDDFHKSSSPISVISSMLRRLERKSTEVPDLLQKSISFLNEAQENLSD- 276
            E+I   L    + F   S      +  + + E    E+ +  ++  +     ++   D 
Sbjct: 343 LEKIEEGLKDENEKFDIES------NEEVEKNEAVKKEIKERAKELKNKFESLKKKFQDL 396

Query: 277 ------AQHEIERSFSEIQYDAQELANIEERLFALRAMSRKYSVSIDQLPELAKKMEEDL 330
                  + +++R  S+I+   +E+     +   L     K  + I       +K + ++
Sbjct: 397 EREDVKREEKLKRLTSKIKKLEKEIEKARRKKSELEKAPEKARIEI-------QKCQTEI 449

Query: 331 ADISEGNEKVVSLERVLYEARQAYDRVAQDISTKRYQFAKMLEK 374
             + E  EK    ER L E   +  +  + I  +  +  K L  
Sbjct: 450 EQLEELLEK---EERELDEILDSLKQETEGIREEIEKLEKELMP 490


>gnl|CDD|35471 KOG0250, KOG0250, KOG0250, DNA repair protein RAD18 (SMC family
          protein) [Replication, recombination and repair].
          Length = 1074

 Score = 35.7 bits (82), Expect = 0.034
 Identities = 16/39 (41%), Positives = 23/39 (58%)

Query: 13 ESLDIDFSAGLSILSGDTGSGKSILLDALILVTGGRGDG 51
           +L I+F   ++ + G+ GSGKS +L AL L  GGR   
Sbjct: 54 SNLLIEFGPRVNFIVGNNGSGKSAILTALTLGLGGRASA 92



 Score = 35.3 bits (81), Expect = 0.047
 Identities = 52/293 (17%), Positives = 108/293 (36%), Gaps = 20/293 (6%)

Query: 172  LKKYQEQKSSSQDVEFLRFSIDELQALA--VQPGEENELVVMRSKILKQERIAVELSSIM 229
             KK +E +     +E L+  ++ ++  A  ++         ++ +I K + +  EL    
Sbjct: 744  KKKEKEIEEKEAPLEKLKEELEHIELEAQELEEYYAAGREKLQGEISKLDALKEELKLRE 803

Query: 230  DDFHKSSSPISVISSMLRRLERKSTEVPDLLQKSISFLNEA---QENLSDAQHEIERSFS 286
            D         S         ++  + + +L QK +  +N      E    A+ E      
Sbjct: 804  DKLR------SAEDEKRHYEDKLKSRLEELKQKEVEKVNLEEPRAEEDQKARTECPEEGI 857

Query: 287  EIQYDAQELANIEERLFALRAMSRKYSVSIDQLPELAKKMEEDLADISEGNEKVVSLERV 346
            EI+   + +A I+  +  L+   +    S+ +L EL + + E   ++ + +E  V+L+ +
Sbjct: 858  EIEALGKTVAEIKREIKRLKRQIQMCEESLGELEELHRGLHEARKELKKEDELKVTLDEL 917

Query: 347  LYEARQAYDRVAQDISTKRYQFAKMLEKNVMAEMPALKLENVCFTVNITSDKEDISPDGI 406
            L    +A +   Q     R    +   +   A    L        +    +++ +S    
Sbjct: 918  LKALGEALESREQKYQKFRKLLTRRATEEFDA---LLGKRGFSGKLEFDHEEKTLSI--- 971

Query: 407  DRVEFYVQTNRGENPGPLMKLASGGELSRFLLALKIVLVDQGSIPTLVFDEVD 459
                  + T+  E      +  SGGE S   + L + L +    P    DE D
Sbjct: 972  ---SVKLPTSGNEKAVRDTRGLSGGERSFSTVCLLLSLWEVMECPFRALDEFD 1021


>gnl|CDD|36197 KOG0979, KOG0979, KOG0979, Structural maintenance of chromosome
           protein SMC5/Spr18, SMC superfamily [Chromatin structure
           and dynamics, Cell cycle control, cell division,
           chromosome partitioning, Replication, recombination and
           repair].
          Length = 1072

 Score = 35.7 bits (82), Expect = 0.036
 Identities = 64/411 (15%), Positives = 145/411 (35%), Gaps = 54/411 (13%)

Query: 3   RLSIYNIVLIESLDIDFSAGLSILSGDTGSGKSILLDALILVTGGR----GDGGLVRRHA 58
           R+ ++N +  +  +      L+++ G  GSGKS ++ A+ L  GG+    G    V  + 
Sbjct: 24  RIELHNFLTYDHTEFLPGPSLNMIIGPNGSGKSSIVCAICLGLGGKPKLLGRAKKVGEYI 83

Query: 59  EKGQVVAVFEISHLPALEILFAEANLTLEKHVILRRVQFPDGRTKAYVNDQVVS----VN 114
           ++G+     EI      E+   +  LT+ + +        D  +K ++ND   +      
Sbjct: 84  KRGEDEGYIEI------ELKDKDETLTITRLISR------DKESKYFINDSATTKSEIEE 131

Query: 115 FMRAVG------------------------SLLIEIHSQHADRSLLDVQGHRKILDSYAD 150
            +                             LL+E         LL    H +++D   D
Sbjct: 132 LVAHFNIQIDNLCQFLPQDKVKEFARLSPIELLVETEKAIGAEELLQY--HIELMDLRED 189

Query: 151 IDLSLCELGTLYRHWCCTADALKKYQEQKSSSQDVEFLRFSIDELQALAVQPGEENELVV 210
                 +L T         D + K ++     ++ E  +  I+ L+    +   E +   
Sbjct: 190 EKSLEDKLTTKTEKLNRLEDEIDKLEKDVERVRERERKKSKIELLEKK--KKWVEYKKHD 247

Query: 211 MRSKILKQ--ERIAVELSSIMDDFHKSSSPISVISSMLRRLERKSTEVPDLLQKSISFLN 268
                 KQ  +R   EL  +  +          + S  +    K ++    L ++++ + 
Sbjct: 248 REYNAYKQAKDRAKKELRKLEKEIKPIEDKKEELESEKKETRSKISQKQRELNEALAKVQ 307

Query: 269 EAQENLSDAQHEIERSFSEIQYDAQELANIEERLFALRAM--SRKYSVSIDQLPE-LAKK 325
           E  E L + + E+E   ++++   +     ++R+   + M    +  +   + PE   ++
Sbjct: 308 EKFEKLKEIEDEVEEKKNKLESLKKAAEKRQKRIEKAKKMILDAQAELQETEDPENPVEE 367

Query: 326 MEEDLADISEGNEKVVSLERVLYEARQ-AYDRVAQDISTKRYQFAKMLEKN 375
            +E + ++ +     +   R   +A Q    ++    + KR          
Sbjct: 368 DQEIMKEVLQKKSSKLRDSRQEIDAEQLKSQKLRDLENKKRKLKQNSDLNR 418


>gnl|CDD|39561 KOG4360, KOG4360, KOG4360, Uncharacterized coiled coil protein
           [Function unknown].
          Length = 596

 Score = 35.5 bits (81), Expect = 0.037
 Identities = 36/165 (21%), Positives = 58/165 (35%), Gaps = 11/165 (6%)

Query: 179 KSSSQDVEFLRFSIDELQALAVQPGEENELVVMRSKILKQERIAVELSSIMDDFHKSSSP 238
            S+     F R  ++ LQ       EEN  +  ++ +LK E +  E         K    
Sbjct: 148 VSNESRSAFQRELLEALQEKLKPLEEENTQLRSKAMLLKTETLTYEE--------KEQQL 199

Query: 239 ISVISSMLRRLERKSTEVPDLLQKSISFLNEAQENLSDAQHEIERSFSEIQYDAQELANI 298
                  LR    ++    + LQ     L+  QE  S    ++     +I+Y   E    
Sbjct: 200 YGDCVKELRDTNTQARSGQEELQSKTKELSRQQEENSKLLSQLVDLQKKIKYLRHE---K 256

Query: 299 EERLFALRAMSRKYSVSIDQLPELAKKMEEDLADISEGNEKVVSL 343
           EE    L+A          +L EL  K  E +  + E  E++  L
Sbjct: 257 EELDEHLQAYKDAQRQLTAELEELEDKYAECMQMLHEAEEELKCL 301


>gnl|CDD|34784 COG5185, HEC1, Protein involved in chromosome segregation,
           interacts with SMC proteins [Cell division and
           chromosome partitioning].
          Length = 622

 Score = 34.7 bits (79), Expect = 0.068
 Identities = 22/144 (15%), Positives = 61/144 (42%)

Query: 225 LSSIMDDFHKSSSPISVISSMLRRLERKSTEVPDLLQKSISFLNEAQENLSDAQHEIERS 284
           L +  D+ ++       IS  ++ L  K   +     K  +++N  ++   +   ++E+ 
Sbjct: 276 LKTQNDNLYEKIQEAMKISQKIKTLREKWRALKSDSNKYENYVNAMKQKSQEWPGKLEKL 335

Query: 285 FSEIQYDAQELANIEERLFALRAMSRKYSVSIDQLPELAKKMEEDLADISEGNEKVVSLE 344
            SEI+   +E+  ++  +  L    RK  +S +Q   + ++ E+   ++ + N +   L 
Sbjct: 336 KSEIELKEEEIKALQSNIDELHKQLRKQGISTEQFELMNQEREKLTRELDKINIQSDKLT 395

Query: 345 RVLYEARQAYDRVAQDISTKRYQF 368
           + +   +     + + +     Q+
Sbjct: 396 KSVKSRKLEAQGIFKSLEKTLRQY 419


>gnl|CDD|31327 COG1132, MdlB, ABC-type multidrug transport system, ATPase and
           permease components [Defense mechanisms].
          Length = 567

 Score = 34.7 bits (79), Expect = 0.068
 Identities = 25/95 (26%), Positives = 35/95 (36%), Gaps = 8/95 (8%)

Query: 404 DGIDRVEFYVQTNRGENPGPLMKLASGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIG 463
           + I  +     T  GE    L    SGG+  R  +A  ++       P L+ DE  S + 
Sbjct: 446 EFIANLPDGYDTIVGERGVNL----SGGQRQRLAIARALLRNP----PILILDEATSALD 497

Query: 464 GAVADAIGYRLKQLSKKIQLLAVTHAPQVAARADR 498
                 I   LK+L K    L + H       ADR
Sbjct: 498 TETEALIQDALKKLLKGRTTLIIAHRLSTIKNADR 532


>gnl|CDD|72998 cd03239, ABC_SMC_head, The structural maintenance of chromosomes
           (SMC) proteins are essential for successful chromosome
           transmission during replication and segregation of the
           genome in all organisms.  SMCs are generally present as
           single proteins in bacteria, and as at least six
           distinct proteins in eukaryotes.  The proteins range in
           size from approximately 110 to 170 kDa, and each has
           five distinct domains: amino- and carboxy-terminal
           globular domains, which contain sequences characteristic
           of ATPases, two coiled-coil regions separating the
           terminal domains , and a central flexible hinge.  SMC
           proteins function together with other proteins in a
           range of chromosomal transactions, including chromosome
           condensation, sister-chromatid cohesion, recombination,
           DNA repair, and epigenetic silencing of gene
           expression..
          Length = 178

 Score = 34.5 bits (79), Expect = 0.079
 Identities = 21/84 (25%), Positives = 38/84 (45%), Gaps = 1/84 (1%)

Query: 426 KLASGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIGGAVADAIGYRLKQLSKKI-QLL 484
           ++ SGGE S   LAL   L +    P  V DE+D+ +       +   +K+++K   Q +
Sbjct: 93  QILSGGEKSLSALALIFALQEIKPSPFYVLDEIDAALDPTNRRRVSDMIKEMAKHTSQFI 152

Query: 485 AVTHAPQVAARADRHFLVYKTNKP 508
            +T   ++   AD+   V   +  
Sbjct: 153 VITLKKEMFENADKLIGVLFVHGV 176



 Score = 33.3 bits (76), Expect = 0.18
 Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 11/66 (16%)

Query: 17 IDFSAGLSILSGDTGSGKSILLDALILVTGGR-----------GDGGLVRRHAEKGQVVA 65
          +  S   + + G  GSGKS ++DA+  V GG+             GG V+       V  
Sbjct: 18 VGGSNSFNAIVGPNGSGKSNIVDAICFVLGGKAAKLRRGSLLFLAGGGVKAGINSASVEI 77

Query: 66 VFEISH 71
           F+ S+
Sbjct: 78 TFDKSY 83


>gnl|CDD|34155 COG4477, EzrA, Negative regulator of septation ring formation [Cell
           division and chromosome partitioning].
          Length = 570

 Score = 34.5 bits (79), Expect = 0.083
 Identities = 29/151 (19%), Positives = 60/151 (39%), Gaps = 6/151 (3%)

Query: 205 ENELVVMRSKILKQERIAVELSSIMDDFHKSSSPISVISSMLRRLERKSTEVPDLLQKSI 264
           E EL  +R    + + +   L  I+++        S +   L  +E+  T++ D  +K  
Sbjct: 343 ETELGSVRKFEKELKELESVLDEILENIEAQEVAYSELQDNLEEIEKALTDIEDEQEKVQ 402

Query: 265 SFLNEAQENLSDAQHEIERSFSEIQYDAQ-----ELANIEERLFALRA-MSRKYSVSIDQ 318
             L   +++  +A+  +ER  S++    +      L  + E   +L      +    + +
Sbjct: 403 EHLTSLRKDELEARENLERLKSKLHEIKRYMEKSNLPGLPETFLSLFFTAGHEIQDLMKE 462

Query: 319 LPELAKKMEEDLADISEGNEKVVSLERVLYE 349
           L E+   ME   A +    E + +LE    E
Sbjct: 463 LSEVPINMEAVSALVDIATEDMNTLEDETEE 493



 Score = 29.8 bits (67), Expect = 2.2
 Identities = 20/87 (22%), Positives = 40/87 (45%), Gaps = 9/87 (10%)

Query: 295 LANIEERLFALRAMSRKYSV-----SIDQLPELAKKMEEDLADISEGNEKVVSLER---- 345
            A++EE LF   A++ K+        ID + +    +EED+  I E   ++V  E     
Sbjct: 80  FADVEEHLFEAEALADKFRFNKAKHEIDDIEQQLTLIEEDIEQILEDLNELVESEEKNSE 139

Query: 346 VLYEARQAYDRVAQDISTKRYQFAKML 372
            +    + Y+ + +D+   R+Q+ +  
Sbjct: 140 EIDHVLELYEELRRDVLANRHQYGEAA 166


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

 Score = 34.0 bits (78), Expect = 0.095
 Identities = 28/116 (24%), Positives = 41/116 (35%), Gaps = 10/116 (8%)

Query: 429 SGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIGGAVADAIGYRLKQLSKK-IQLLAVT 487
           SGG+  R LLA    L     +  L+ DE  +G+  A    I   LK+L ++   +L VT
Sbjct: 141 SGGQKQRVLLAR--ALAQNPDL--LLLDEPFTGVDVAGQKEIYDLLKELRQEGKTVLMVT 196

Query: 488 HAP-QVAARADRHFLVYKT----NKPDDTQRIETYVAVLTPQERREEIARMLAGSH 538
           H    V A  DR   + +       P++    E                      H
Sbjct: 197 HDLGLVMAYFDRVICLNRHLIASGPPEEVLTEENLEKAFGGSLAHALAGYRHHHDH 252


>gnl|CDD|33393 COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD
          family [DNA replication, recombination, and repair].
          Length = 581

 Score = 33.4 bits (76), Expect = 0.15
 Identities = 21/48 (43%), Positives = 28/48 (58%)

Query: 3  RLSIYNIVLIESLDIDFSAGLSILSGDTGSGKSILLDALILVTGGRGD 50
          R+ I N   I  L ++F  GL++L G+  SGKS LLDAL L+     D
Sbjct: 5  RVKIKNFRGINRLSLEFEEGLNVLIGENNSGKSSLLDALRLLLDPESD 52



 Score = 28.4 bits (63), Expect = 5.1
 Identities = 8/38 (21%), Positives = 14/38 (36%)

Query: 474 LKQLSKKIQLLAVTHAPQVAARADRHFLVYKTNKPDDT 511
           L  L   +Q +  TH+P + + AD   +          
Sbjct: 326 LNNLPLGLQRIVTTHSPHLLSLADLDSICRLVRVSSRV 363


>gnl|CDD|36151 KOG0933, KOG0933, KOG0933, Structural maintenance of chromosome
           protein 2 (chromosome condensation complex Condensin,
           subunit E) [Chromatin structure and dynamics, Cell cycle
           control, cell division, chromosome partitioning].
          Length = 1174

 Score = 33.0 bits (75), Expect = 0.20
 Identities = 33/165 (20%), Positives = 62/165 (37%), Gaps = 11/165 (6%)

Query: 177 EQKSSSQDVEFLRFSIDELQALAVQPGEENELVVMRSKILKQERI----AVELSSIMDDF 232
           E K  S   E  R             GEE +L  +R  I +  +        ++ + + +
Sbjct: 300 EDKLDSLQNEITREETSLNLKKETLNGEEEKLEEIRKNIEEDRKKLKEKEKAMAKVEEGY 359

Query: 233 HKSSSPISVISSMLRRLERKSTEVPDLLQKS-------ISFLNEAQENLSDAQHEIERSF 285
            K        S +L + E     +   L  +          L +A+  LS+A  EI+++ 
Sbjct: 360 EKLKEAFQEDSKLLEKAEELVESLTAGLSSNEDEEKTLEDQLRDAKITLSEASTEIKQAK 419

Query: 286 SEIQYDAQELANIEERLFALRAMSRKYSVSIDQLPELAKKMEEDL 330
            ++++  +EL   E  L    A   K    +D L    +K+++ L
Sbjct: 420 LKLEHLRKELKLREGELATASAEYVKDIEELDALQNEVEKLKKRL 464



 Score = 29.5 bits (66), Expect = 2.2
 Identities = 64/342 (18%), Positives = 130/342 (38%), Gaps = 26/342 (7%)

Query: 176  QEQKSSSQDVEFLRFSIDELQALAVQPGEENELVVMRSKILKQERIAVELSSIMDDFHKS 235
            +E  S  Q +E L   I  L         ++EL  + +K+ K E+   +  + + D    
Sbjct: 829  KEISSLKQQLEQLEKQISSL---------KSELGNLEAKVDKVEKDVKKAQAELKDQKAK 879

Query: 236  SSPIS-VISSMLRRLERKSTEVPDL---LQKSISFLNEAQENLSDAQHEIERSFSEIQYD 291
               I   IS +L   E+  +E  D     +K    + + +   ++A+ E+E+   + ++ 
Sbjct: 880  QRDIDTEISGLLTSQEKCLSEKSDGELERKKLEHEVTKLESEKANARKEVEKLLKKHEWI 939

Query: 292  AQELANIEERLFALRAMSRKYSVSIDQLPELAKKMEEDLADISEGNEKVVSL----ERVL 347
              E     ++       S     + ++L +L +K E+    +   N K + +    E   
Sbjct: 940  GDEKRLFGKKGTDYDFESYDPHEAREELKKLQEKKEKLEKTV---NPKNMDMLERAEEKE 996

Query: 348  YEARQAYDRVAQDISTKRYQFAKMLEKNVMAEMPALKLENVCF-----TVNITSDKEDIS 402
               +   + + +D S  +    K+ EK       A +  N  F     T+   +  +   
Sbjct: 997  AALKTKKEIIEKDKSKIKKTIEKLDEKKREELNKAWEKVNKDFGSIFSTLLPGAMAKLEP 1056

Query: 403  PDGIDRVEFY-VQTNRGENPGPLMKLASGGELSRFLLALKIVLVDQGSIPTLVFDEVDSG 461
            P+G   ++   V+   G      +   SGG+ S   L+L + ++     P  + DEVD+ 
Sbjct: 1057 PEGKTVLDGLEVKVKFGGIWKESLSELSGGQRSLVALSLILAMLKFKPAPLYILDEVDAA 1116

Query: 462  IGGAVADAIGYRLKQLSKKIQLLAVTHAPQVAARADRHFLVY 503
            +  +    IG  +K      Q + V+    +   A+  F   
Sbjct: 1117 LDLSHTQNIGRMIKTHFTHSQFIVVSLKEGMFNNANVLFRTR 1158


>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 = 33.1 bits (76), Expect = 0.21
 Identities = 19/70 (27%), Positives = 30/70 (42%), Gaps = 4/70 (5%)

Query: 429 SGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIGGAVADAIGYRLKQLSKKIQLLAVTH 488
           SGG+  R  +A+   L+    I  L+ DE  S +       I   L+ L+K   ++ + H
Sbjct: 98  SGGQRQR--IAIARALLRDPPI--LILDEATSALDPETEALILEALRALAKGKTVIVIAH 153

Query: 489 APQVAARADR 498
                  ADR
Sbjct: 154 RLSTIRDADR 163


>gnl|CDD|73038 cd03279, ABC_sbcCD, SbcCD and other Mre11/Rad50 (MR) complexes
          are implicated in the metabolism of DNA ends. They
          cleave ends sealed by hairpin structures and are
          thought to play a role in removing protein bound to DNA
          termini..
          Length = 213

 Score = 32.1 bits (73), Expect = 0.36
 Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 5/44 (11%)

Query: 3  RLSIYNI-VLIESLDIDFS----AGLSILSGDTGSGKSILLDAL 41
          +L + N     E   IDF+     GL ++ G TG+GKS +LDA+
Sbjct: 5  KLELKNFGPFREEQVIDFTGLDNNGLFLICGPTGAGKSTILDAI 48


>gnl|CDD|35470 KOG0249, KOG0249, KOG0249, LAR-interacting protein and related
           proteins [General function prediction only].
          Length = 916

 Score = 32.0 bits (72), Expect = 0.39
 Identities = 38/196 (19%), Positives = 84/196 (42%), Gaps = 10/196 (5%)

Query: 182 SQDVEFLRFSIDELQALAVQPGEENELVVMRSKILKQERIAVELSSIMDDFHKSSSPISV 241
             +    +   D  +A+A +   E  +  +  + L  +R   E +SI D   K  + ++ 
Sbjct: 46  KAEEMNTKLQRDIREAMAQKEDMEERITTLEKRFLNAQR---ESTSIHDLNDKLENELAN 102

Query: 242 ISSMLRRLERKSTEVPDLLQKSISFLNE--AQENLSDAQHEIERSFSEIQYDAQELANIE 299
             + LR+ E K+  + + L+ +   L +    E L + + E+ +  + +    +   NIE
Sbjct: 103 KDADLRQNEEKNRSLQERLELAEPKLQQSLRAETLPEVEAELAQRNAALTKAEEHSGNIE 162

Query: 300 ERLFALRAMSRKYSVSIDQLPELAKKMEED---LADISEGNEKVVSLERVLYEARQAYDR 356
           ER   L     + +  + +  +  K  EE    L+D  +   ++   ER+   A +  +R
Sbjct: 163 ERTRKLEEQLEELNAELQRARQREKMNEEHNKRLSDTVDERLQLHLKERM--AALEDKNR 220

Query: 357 VAQDISTKRYQFAKML 372
           + Q++ + + Q  +M 
Sbjct: 221 LEQELESVKKQLEEMR 236


>gnl|CDD|35464 KOG0243, KOG0243, KOG0243, Kinesin-like protein [Cytoskeleton].
          Length = 1041

 Score = 32.3 bits (73), Expect = 0.40
 Identities = 53/322 (16%), Positives = 122/322 (37%), Gaps = 25/322 (7%)

Query: 172 LKKYQEQKSSSQDV-EFLRFSIDELQALAVQPGEENELVVMRSKILKQERIAVELSSIMD 230
           LK   E   +  ++ E L+   ++L++      +  EL  ++ ++ + +    E   I+ 
Sbjct: 464 LKDLTELYMNQLEIKELLKEEKEKLKSKLQN--KNKELESLKEELQQAKATLKEEEEIIS 521

Query: 231 DFHKSSSPISVISSMLRRLERKST-EVPDLLQKSISFLNEAQENLSDAQHEIERSFSEIQ 289
              KS   +   ++ LRR   +S  ++  L +K         +N                
Sbjct: 522 QQEKSEEKLVDRATKLRRSLEESQDDLSSLFEKLDRKDRLDDDNQEVIDD---------- 571

Query: 290 YDAQELANIEERLFALRAMSRKYSVSIDQLPELAKKMEEDLADISEGNEKV---VSLERV 346
           + +Q   N+      + + S +    I QL  +  +ME  L+  S+  E +   +S +R 
Sbjct: 572 FQSQLSENLSTLHGLVASSSSQQ---ISQLTTMLAQMESFLSAKSKATEIMKTKISKDRD 628

Query: 347 LY-EARQAYDRVAQDISTKRYQFAKMLEKNVMAEMPALKLENVCFTVNITSDK--EDISP 403
           +  E  ++  ++ + +        +++  ++ +     +LE++  T+  T+D   ++IS 
Sbjct: 629 ILSEVLESLQQLQEVLKKDSESCLEVINSSITSS--INELESMLETIANTADDLLQNISS 686

Query: 404 DGIDRVEFYVQTNRGENPGPLMKLASGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIG 463
              ++ E        E    ++   S  ELS         L +Q    T +F E +  + 
Sbjct: 687 RLSNQQEILSLFANQELQELVLSQDSAQELSELTSTFFQTLDNQAEKLTNLFSEANISLS 746

Query: 464 GAVADAIGYRLKQLSKKIQLLA 485
             ++            + QL+ 
Sbjct: 747 QKLSSFQKKFESIAEDEKQLVE 768


>gnl|CDD|37484 KOG2273, KOG2273, KOG2273, Membrane coat complex Retromer, subunit
           VPS5/SNX1, Sorting nexins, and related PX
           domain-containing proteins [Intracellular trafficking,
           secretion, and vesicular transport].
          Length = 503

 Score = 32.0 bits (72), Expect = 0.44
 Identities = 34/215 (15%), Positives = 90/215 (41%), Gaps = 13/215 (6%)

Query: 172 LKKYQEQKSSSQDVEFLRFSIDELQALAVQPGEENELVVMRSKILKQERIAVELSSIMDD 231
           L  +++ K S ++    +  ID+L+    +  ++ + +V         +   EL+S + +
Sbjct: 263 LPSFKKFKESDKEFTEKKEKIDKLEQQLKKLSKQVQRLV---------KRRRELASNLAE 313

Query: 232 FHKSSSPISVISSMLRRLERKSTEVPDLLQKSISFLNEAQENLSDAQHEIERSFSEIQYD 291
             K+ + +S +      L    + +  +  +S+S L E      D++   E+    I+Y 
Sbjct: 314 LGKALAQLSALEGETDELSEALSGLAKV-IESLSKLLEKLTAEKDSKKLAEQLREYIRYL 372

Query: 292 AQELANIEERLFALRAMSRKYSVSIDQLPELAKKMEEDLADISEGNEKVVSLERVLYEAR 351
               +  E+R  AL+ +       +    E   K+++     S G +K+   E+ + +  
Sbjct: 373 ESVKSLFEQRSKALQKLQEAQRE-LSSKKEQLSKLKKKN-RSSFGFDKIDLAEKEIEKLE 430

Query: 352 QAYDRVAQDISTKRYQFAKMLEKNVMAEMPALKLE 386
           +  + + + ++ K  +  + + + + AE+   +  
Sbjct: 431 EKVNELEELLALKELELDE-ISERIRAELERFEES 464


>gnl|CDD|32260 COG2077, Tpx, Peroxiredoxin [Posttranslational modification,
           protein turnover, chaperones].
          Length = 158

 Score = 32.1 bits (73), Expect = 0.44
 Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 12/64 (18%)

Query: 130 HADRSLLDVQGHRKILDSYADIDLSLCELGTLYRHWCCTADALKKYQEQKSSSQDVEFLR 189
             D SL D  G +K++  +  ID  +C                +K+ E+ +   +   L 
Sbjct: 34  LNDVSLADFAGKKKVISVFPSIDTPVCATQV------------RKFNEEAAKLGNTVVLC 81

Query: 190 FSID 193
            S+D
Sbjct: 82  ISMD 85


>gnl|CDD|36194 KOG0976, KOG0976, KOG0976, Rho/Rac1-interacting serine/threonine
           kinase Citron [Signal transduction mechanisms].
          Length = 1265

 Score = 32.0 bits (72), Expect = 0.46
 Identities = 46/226 (20%), Positives = 99/226 (43%), Gaps = 22/226 (9%)

Query: 170 DALKKYQEQKSSSQDVEFLRFSIDELQALAVQPGEENELVVMRSKILKQERIAV---ELS 226
           D  K+  + ++  QD+   R ++ E  +L  + G    +++ +SK +  +   +   +++
Sbjct: 38  DLKKRLLDAENIIQDLRSERDALHE--SLVDKAGLNESVIIEQSKKVSTQETRIYRRDVN 95

Query: 227 SIMDDFHKSSSPISVISSMLRRLERKSTEVPDLLQKSISFLNEAQ---ENLSDAQHEIER 283
            + DD     S I ++ +   RLE +  ++ D +Q +     E +   ENL+   H++E 
Sbjct: 96  LLEDDLKHHESQIRILQNKCLRLEMEKQKLQDTIQGAQDDKKENEIEIENLNSRLHKLED 155

Query: 284 SFS----EIQYDAQELANIEERLFALRA-MSRKYSVSIDQLPELAKKMEEDLADISEGNE 338
             S    +I    ++L +  E L         K + +  +   L +K+E+   D+ E ++
Sbjct: 156 ELSAKAHDIFMIGEDLHDKNEELNEFNMEFQTKLAEANREKKALEEKLEKFKEDLIEKDQ 215

Query: 339 KVVSL-------ERVLYEARQAYDRVAQDISTKRYQFAKMLEKNVM 377
           K + L       ++VL E  Q   +  +   T   +   M+E+  M
Sbjct: 216 KSLELHKDQENTQKVLKEVMQLSSQ--KQTLTPLRKTCSMIEEQDM 259


>gnl|CDD|34522 COG4913, COG4913, Uncharacterized protein conserved in bacteria
          [Function unknown].
          Length = 1104

 Score = 32.0 bits (72), Expect = 0.51
 Identities = 15/50 (30%), Positives = 31/50 (62%), Gaps = 2/50 (4%)

Query: 1  MTRLSIYNIVLIESLDIDFSAGLSILSGDTGSGKSILLDAL--ILVTGGR 48
          ++R+ + N     ++DI  +    +++G +GSGKS L+DA+  +L+  G+
Sbjct: 17 LSRIQLINWGTFHTVDIPVTREGILVTGGSGSGKSTLIDAITAVLLPQGK 66


>gnl|CDD|34256 COG4637, COG4637, Predicted ATPase [General function prediction
          only].
          Length = 373

 Score = 31.9 bits (72), Expect = 0.54
 Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 2/66 (3%)

Query: 1  MTRLSIYNIVLIESLDIDFSAGLSILSGDTGSGKSILLDALILVTGGRGDGGLVRRHAEK 60
          +  + + N     SLD++    ++++ G  G+GKS   DAL L+      G L +    +
Sbjct: 3  LVSIKVKNYRSFRSLDLEIR-RVNVIIGANGAGKSNFYDALRLL-ADAVRGNLQQALQRE 60

Query: 61 GQVVAV 66
          G +  V
Sbjct: 61 GGLNEV 66


>gnl|CDD|114288 pfam05557, MAD, Mitotic checkpoint protein.  This family consists
           of several eukaryotic mitotic checkpoint (Mitotic arrest
           deficient or MAD) proteins. The mitotic spindle
           checkpoint monitors proper attachment of the bipolar
           spindle to the kinetochores of aligned sister chromatids
           and causes a cell cycle arrest in prometaphase when
           failures occur. Multiple components of the mitotic
           spindle checkpoint have been identified in yeast and
           higher eukaryotes. In S.cerevisiae, the existence of a
           Mad1-dependent complex containing Mad2, Mad3, Bub3 and
           Cdc20 has been demonstrated.
          Length = 722

 Score = 31.4 bits (71), Expect = 0.67
 Identities = 49/238 (20%), Positives = 86/238 (36%), Gaps = 32/238 (13%)

Query: 169 ADALKKYQEQKSSSQDVEFLRFSIDELQALAVQPGEENELVVMRSKILKQERIAVELSSI 228
           A  L +  E++        L   +  L+ L  +   E       +K+LK +  A  L   
Sbjct: 95  ASTLAENYERELDRN--LELEVRLKALEELEKKAENEAAEAEEEAKLLKDKLDAESLKLQ 152

Query: 229 MDDFHKSSSPISVISSMLRRLERKSTEVPDLLQKSISFLNEAQENLSDAQHEIERSFSEI 288
            +   +       IS +   L          +Q        A   L   + E+E    ++
Sbjct: 153 NEKEDQLKEAKESISRIKNDLSE--------MQCRAQ---NADTELKLLESELEELREQL 201

Query: 289 QYDAQELANIEERLFALR---AMSRKYSVSIDQLPELAKKMEEDLADISEGNEKVVSLER 345
           +   +ELA  E++L +L    A S   SV I  L E  K+ E+D   +    E+++ +  
Sbjct: 202 EECQKELAEAEKKLQSLTSEQASSADNSVKIKHLEEELKRYEQDAEVVKSMKEQLLQIPE 261

Query: 346 VLYEARQAYDRVAQ----------------DISTKRYQFAKMLEKNVMAEMPALKLEN 387
           +  E     +   +                D+ ++  +F KM EK    E+   KLEN
Sbjct: 262 LERELAALREENRKLRSMKEDNELLKEELEDLQSRLERFEKMREKLADLELEKEKLEN 319


>gnl|CDD|33919 COG4181, COG4181, Predicted ABC-type transport system involved in
           lysophospholipase L1 biosynthesis, ATPase component
           [Secondary metabolites biosynthesis, transport, and
           catabolism].
          Length = 228

 Score = 31.4 bits (71), Expect = 0.70
 Identities = 27/74 (36%), Positives = 33/74 (44%), Gaps = 6/74 (8%)

Query: 429 SGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIGGAVADAIGYRLKQLSKK--IQLLAV 486
           SGGE  R  LA        G    L  DE    +  A  D I   L  L+++    L+ V
Sbjct: 148 SGGEQQRVALARAFA----GRPDVLFADEPTGNLDRATGDKIADLLFALNRERGTTLVLV 203

Query: 487 THAPQVAARADRHF 500
           TH PQ+AAR DR  
Sbjct: 204 THDPQLAARCDRQL 217


>gnl|CDD|39873 KOG4674, KOG4674, KOG4674, Uncharacterized conserved coiled-coil
           protein [Function unknown].
          Length = 1822

 Score = 31.1 bits (70), Expect = 0.70
 Identities = 39/238 (16%), Positives = 86/238 (36%), Gaps = 12/238 (5%)

Query: 134 SLLDVQGHRKILDSYADIDLSLCELG---TLYRHWCCTADALKKYQEQKSSSQDVEFLRF 190
            L+DV   +K+     D +    E G     +       +      EQ+ S    +    
Sbjct: 19  PLVDVDVFKKLPKKSKDFESLKDEDGKTEVNHEQQLSELEKKILRLEQRLSDLSRQAKLL 78

Query: 191 SIDELQALAVQPGEENELVVMRSKILKQERIAVELSSIMDDFHKSSSPISVISSMLRRLE 250
             +            +E   +  +I   +    +L     +  +          ++  LE
Sbjct: 79  RNELSDLRNELEQLSSERSNLSWEIDALKLENSQLRRAKSELQEQKR------QLMELLE 132

Query: 251 RKSTEVPDLLQKSISFLNEAQENLSDAQHEIERSFSEIQYDAQELANIEERLFALRAMSR 310
           R+  E+ + L+     LN+  ++ +    E+E    E Q +       EERL   +++  
Sbjct: 133 RQKAEL-EALESENKDLNDQLKSSTKTLSELEARLQETQSEDVSSQLKEERLEQEKSLLE 191

Query: 311 KYSVSIDQLPELAKKMEEDLADISEGNEKVVSLERVLYEARQAYDRVAQDISTKRYQF 368
             +  + +  EL+K  E+ L+   E + +V  LE  L + +++   + +   + + Q 
Sbjct: 192 SENKWLSR--ELSKVNEKLLSLRREHSIEVEQLEEKLSDLKESLAELQEKNKSLKQQN 247


>gnl|CDD|33672 COG3883, COG3883, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 265

 Score = 31.1 bits (70), Expect = 0.74
 Identities = 18/75 (24%), Positives = 37/75 (49%)

Query: 258 DLLQKSISFLNEAQENLSDAQHEIERSFSEIQYDAQELANIEERLFALRAMSRKYSVSID 317
           D +Q   S L+E Q+   + Q+EIE   ++I+    ++  +++ +   +A  +K    I 
Sbjct: 31  DKIQNQDSKLSELQKEKKNIQNEIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIA 90

Query: 318 QLPELAKKMEEDLAD 332
           +L E   + +E L  
Sbjct: 91  ELKENIVERQELLKK 105


>gnl|CDD|73033 cd03274, ABC_SMC4_euk, Eukaryotic SMC4 proteins; SMC proteins are
           large (approximately 110 to 170 kDa), and each is
           arranged into five recognizable domains.  Amino-acid
           sequence homology of SMC proteins between species is
           largely confined to the amino- and carboxy-terminal
           globular domains.  The amino-terminal domain contains a
           'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the
           single-letter amino-acid code), which by mutational
           studies has been shown to be essential in several
           proteins.  The carboxy-terminal domain contains a
           sequence (the DA-box) that resembles a 'Walker B' motif,
           and a motif with homology to the signature sequence of
           the ATP-binding cassette (ABC) family of ATPases.  The
           sequence homology within the carboxy-terminal domain is
           relatively high within the SMC1-SMC4 group, whereas SMC5
           and SMC6 show some divergence in both of these
           sequences.  In eukaryotic cells, the proteins are found
           as heterodimers of SMC1 paired with SMC3, SMC2 with
           SMC4, and SMC5 with SMC6 (formerly known as Rad18)..
          Length = 212

 Score = 31.0 bits (70), Expect = 0.91
 Identities = 23/78 (29%), Positives = 36/78 (46%)

Query: 429 SGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIGGAVADAIGYRLKQLSKKIQLLAVTH 488
           SGGE +   LAL   L      P  V DE+D+ +       +   +K+ +K  Q + ++ 
Sbjct: 129 SGGEKTLSSLALVFALHHYKPTPLYVMDEIDAALDFRNVSIVANYIKERTKNAQFIVISL 188

Query: 489 APQVAARADRHFLVYKTN 506
              +   ADR   +YKTN
Sbjct: 189 RNNMFELADRLVGIYKTN 206



 Score = 27.9 bits (62), Expect = 8.5
 Identities = 12/30 (40%), Positives = 18/30 (60%)

Query: 19 FSAGLSILSGDTGSGKSILLDALILVTGGR 48
          F    S + G  GSGKS ++D+++ V G R
Sbjct: 23 FHKSFSAIVGPNGSGKSNVIDSMLFVFGFR 52


>gnl|CDD|73005 cd03246, ABCC_Protease_Secretion, This family represents the ABC
           component of the protease secretion system PrtD, a
           60-kDa integral membrane protein sharing 37% identity
           with HlyB, the ABC component of the alpha-hemolysin
           secretion pathway, in the C-terminal domain.  They
           export degradative enzymes by using a type I protein
           secretion system and  lack an N-terminal signal peptide,
           but contain a C-terminal secretion signal.  The Type I
           secretion apparatus is made up of three components, an
           ABC transporter, a membrane fusion protein (MFP), and an
           outer membrane protein (OMP).  For the HlyA transporter
           complex, HlyB (ABC transporter) and HlyD (MFP) reside in
           the inner membrane of E. coli.  The OMP component is
           TolC, which is thought to interact with the MFP to form
           a continuous channel across the periplasm from the
           cytoplasm to the exterior.  HlyB belongs to the family
           of ABC transporters, which are ubiquitous, ATP-dependent
           transmembrane pumps or channels.  The spectrum of
           transport substrates ranges from inorganic ions,
           nutrients such as amino acids, sugars, or peptides,
           hydrophobic drugs, to large polypeptides, such as HlyA..
          Length = 173

 Score = 30.5 bits (69), Expect = 1.2
 Identities = 21/71 (29%), Positives = 29/71 (40%), Gaps = 5/71 (7%)

Query: 429 SGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIGGAVADAIGYRLKQLSKK-IQLLAVT 487
           SGG+  R  LA    L     I  LV DE +S +      A+   +  L       + + 
Sbjct: 98  SGGQRQRLGLAR--ALYGNPRI--LVLDEPNSHLDVEGERALNQAIAALKAAGATRIVIA 153

Query: 488 HAPQVAARADR 498
           H P+  A ADR
Sbjct: 154 HRPETLASADR 164


>gnl|CDD|72982 cd03223, ABCD_peroxisomal_ALDP, Peroxisomal ATP-binding cassette
          transporter (Pat) is involved in the import of very
          long-chain fatty acids (VLCFA) into the peroxisome.
          The peroxisomal membrane forms a permeability barrier
          for a wide variety of metabolites required for and
          formed during fatty acid beta-oxidation.  To
          communicate with the cytoplasm and mitochondria,
          peroxisomes need dedicated proteins to transport such
          hydrophilic molecules across their membranes.  X-linked
          adrenoleukodystrophy (X-ALD) is caused by mutations in
          the ALD gene, which encodes ALDP (adrenoleukodystrophy
          protein ), a peroxisomal integral membrane protein that
          is a member of the ATP-binding cassette (ABC)
          transporter protein family.  The disease is
          characterized by a striking and unpredictable variation
          in phenotypic expression.  Phenotypes include the
          rapidly progressive childhood cerebral form (CCALD),
          the milder adult form, adrenomyeloneuropathy (AMN), and
          variants without neurologic involvement (i.e.
          asymptomatic)..
          Length = 166

 Score = 30.5 bits (69), Expect = 1.2
 Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 1/35 (2%)

Query: 8  NIVLIESLDIDFSAGLSIL-SGDTGSGKSILLDAL 41
            VL++ L  +   G  +L +G +G+GKS L  AL
Sbjct: 13 GRVLLKDLSFEIKPGDRLLITGPSGTGKSSLFRAL 47


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

 Score = 30.3 bits (68), Expect = 1.4
 Identities = 31/148 (20%), Positives = 53/148 (35%), Gaps = 35/148 (23%)

Query: 11  LIESLDIDFSAG-LSILSGDTGSGKSILLDAL-------------ILVTGGRGDGGLVRR 56
           +++ +      G L  + G +GSGK+ LL+AL             IL+ G   D    R+
Sbjct: 45  ILKGVSGTAKPGELLAIMGPSGSGKTTLLNALAGRLNGGLKLSGEILLNGRPRDSRSFRK 104

Query: 57  HAEKGQVVAVFEISHLPALEILFAEANLTLEKHVILRRVQFPDGRTKAYVNDQVVSVNFM 116
            +   Q   V  +  L   E L   A L L           P   +K    ++       
Sbjct: 105 ISGYVQQDDVL-LPTLTVRETLRFSALLRL-----------PSSLSKEEKRER------- 145

Query: 117 RAVGSLLIEIHSQHADRSLLDVQGHRKI 144
             V  ++ E+  +    +L+   G R +
Sbjct: 146 --VEEVISELGLEKCADTLIGNPGIRGL 171


>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 = 1.5
 Identities = 12/33 (36%), Positives = 20/33 (60%), Gaps = 1/33 (3%)

Query: 11 LIESLDIDFSAG-LSILSGDTGSGKSILLDALI 42
           ++ ++++   G L  + G  GSGKS LL AL+
Sbjct: 20 TLKDINLEVPKGELVAIVGPVGSGKSSLLSALL 52


>gnl|CDD|35283 KOG0060, KOG0060, KOG0060, Long-chain acyl-CoA transporter, ABC
           superfamily (involved in peroxisome organization and
           biogenesis) [Lipid transport and metabolism, General
           function prediction only].
          Length = 659

 Score = 30.3 bits (68), Expect = 1.6
 Identities = 13/35 (37%), Positives = 23/35 (65%), Gaps = 1/35 (2%)

Query: 8   NIVLIESLDIDFSAGLSIL-SGDTGSGKSILLDAL 41
             +LIE+L ++  +G ++L +G +G GK+ LL  L
Sbjct: 447 GDLLIENLSLEVPSGQNLLITGPSGCGKTSLLRVL 481


>gnl|CDD|33697 COG3910, COG3910, Predicted ATPase [General function prediction
          only].
          Length = 233

 Score = 30.3 bits (68), Expect = 1.6
 Identities = 15/48 (31%), Positives = 28/48 (58%), Gaps = 2/48 (4%)

Query: 7  YNIVLIESLD--IDFSAGLSILSGDTGSGKSILLDALILVTGGRGDGG 52
          +++     L+  ++F A ++ ++G+ GSGKS LL+A+    G    GG
Sbjct: 21 FSLPAFRHLEERLEFRAPITFITGENGSGKSTLLEAIAAGMGFNAAGG 68


>gnl|CDD|34081 COG4372, COG4372, Uncharacterized protein conserved in bacteria
           with the myosin-like domain [Function unknown].
          Length = 499

 Score = 30.1 bits (67), Expect = 1.8
 Identities = 31/222 (13%), Positives = 68/222 (30%), Gaps = 12/222 (5%)

Query: 169 ADALKKYQEQKSSSQDVEFLRFSIDELQALAVQPGEENELVVMRSKILKQERIAV--ELS 226
                   E  ++  +        +  ++   +  +E E V       +Q       EL+
Sbjct: 81  PQLRALRTELGTAQGEKRAAETEREAARSELQKARQEREAVRQELAAARQNLAKAQQELA 140

Query: 227 SIMDDFHKSSSPISVISSMLRRLERKSTEV---PDLLQKSISFLNEAQENLSDAQHEIE- 282
            +        + +  ++   R+LE ++  +      LQ S + L     +L     +IE 
Sbjct: 141 RLTKQAQDLQTRLKTLAEQRRQLEAQAQSLQASQKQLQASATQLKSQVLDLKLRSAQIEQ 200

Query: 283 ------RSFSEIQYDAQELANIEERLFALRAMSRKYSVSIDQLPELAKKMEEDLADISEG 336
                    +  Q   +ELA             ++    I Q  +      E + +    
Sbjct: 201 EAQNLATRANAAQARTEELARRAAAAQQTAQAIQQRDAQISQKAQQIAARAEQIRERERQ 260

Query: 337 NEKVVSLERVLYEARQAYDRVAQDISTKRYQFAKMLEKNVMA 378
            +++ + +  L +     +   Q     R Q A      V+A
Sbjct: 261 LQRLETAQARLEQEVAQLEAYYQAYVRLRQQAAATQRGQVLA 302


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

 Score = 29.7 bits (67), Expect = 1.9
 Identities = 25/76 (32%), Positives = 36/76 (47%), Gaps = 14/76 (18%)

Query: 429 SGGELSRFLLAL------KIVLVDQGSIPTLVFDEVDSGIGGAVADAIGYRLKQLSKKIQ 482
           SGG+  R  +A       KI+L D+   PT     +DS     V + +    K+  K I 
Sbjct: 144 SGGQQQRVAIARALINNPKIILADE---PT---GNLDSKTAKEVLELLRELNKERGKTI- 196

Query: 483 LLAVTHAPQVAARADR 498
            + VTH P++A  ADR
Sbjct: 197 -IMVTHDPELAKYADR 211


>gnl|CDD|35385 KOG0163, KOG0163, KOG0163, Myosin class VI heavy chain
            [Cytoskeleton].
          Length = 1259

 Score = 29.6 bits (66), Expect = 2.1
 Identities = 24/163 (14%), Positives = 52/163 (31%), Gaps = 12/163 (7%)

Query: 242  ISSMLRRLERKSTEVPDLLQKSISFLNEAQENLSDAQHEIERSFSEIQYDAQELANIEER 301
            ++S      +   ++   L        E  E L   Q   E      + + +     EE+
Sbjct: 894  MNSEYDVAVKNYEKLVKRLDSKEQQQIEELERLRKIQELAEAERKRREAEEKRRREEEEK 953

Query: 302  LFALRAMSRKYSVSIDQLPELAKKMEEDLADISEGNEKVVSLERVLYEARQAYDRVAQDI 361
              A   M            E  +K EE+     E  E+ ++LE     A++A +   +  
Sbjct: 954  KRAKAEM------------ETKRKAEEEQRKAQEEEERRLALELQEQLAKEAEEEAKRQN 1001

Query: 362  STKRYQFAKMLEKNVMAEMPALKLENVCFTVNITSDKEDISPD 404
              ++ +    L   +         ++      + +D   + P+
Sbjct: 1002 QLEQERRDHELALRLANSDGGQVEDSPPVIRALVNDASPMGPN 1044


>gnl|CDD|34592 COG4987, CydC, ABC-type transport system involved in cytochrome bd
           biosynthesis, fused ATPase and permease components
           [Energy production and conversion / Posttranslational
           modification, protein turnover, chaperones].
          Length = 573

 Score = 29.8 bits (67), Expect = 2.2
 Identities = 22/70 (31%), Positives = 31/70 (44%), Gaps = 4/70 (5%)

Query: 429 SGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIGGAVADAIGYRLKQLSKKIQLLAVTH 488
           SGGE  R  LA + +L D    P  + DE   G+       +   L + ++   LL VTH
Sbjct: 476 SGGERRRLALA-RALLHDA---PLWLLDEPTEGLDPITERQVLALLFEHAEGKTLLMVTH 531

Query: 489 APQVAARADR 498
             +   R DR
Sbjct: 532 RLRGLERMDR 541


>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 = 29.5 bits (66), Expect = 2.3
 Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 9/78 (11%)

Query: 3  RLSIYNIVLIESLDIDFSAG-LSILSGDTGSGKSILLDALIL---VTGGR-----GDGGL 53
                   ++++ +   AG +  L G  GSGKS LL A+      T G       D   
Sbjct: 6  SFRYGGRTALDNVSLTLKAGEIVALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAK 65

Query: 54 VRRHAEKGQVVAVFEISH 71
          +     + ++  V ++S 
Sbjct: 66 LPLEELRRRIGYVPQLSG 83


>gnl|CDD|32455 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain
           an N-terminal double-glycine peptidase domain [Defense
           mechanisms].
          Length = 709

 Score = 29.4 bits (66), Expect = 2.4
 Identities = 17/70 (24%), Positives = 27/70 (38%), Gaps = 4/70 (5%)

Query: 429 SGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIGGAVADAIGYRLKQLSKKIQLLAVTH 488
           SGG+  R  LA  ++         L+ DE  S +       I   L Q+ +   ++ + H
Sbjct: 611 SGGQRQRLALARALL----SKPKILLLDEATSALDPETEAIILQNLLQILQGRTVIIIAH 666

Query: 489 APQVAARADR 498
                  ADR
Sbjct: 667 RLSTIRSADR 676


>gnl|CDD|72994 cd03235, ABC_Metallic_Cations, ABC component of the metal-type
           transporters.  This family includes transporters
           involved in the uptake of various metallic cations such
           as iron, manganese, and zinc.  The ATPases of this group
           of transporters are very similar to members of
           iron-siderophore uptake family suggesting that they
           share a common ancestor.  The best characterized
           metal-type ABC transporters are the YfeABCD system of Y.
           pestis, the SitABCD system of Salmonella enterica
           serovar Typhimurium, and the SitABCD transporter of
           Shigella flexneri.  Moreover other uncharacterized
           homologs of these metal-type transporters are mainly
           found in pathogens like Haemophilus or enteroinvasive E.
           coli isolates..
          Length = 213

 Score = 29.7 bits (67), Expect = 2.4
 Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 429 SGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIGGAVADAIGYRLKQLSKK-IQLLAVT 487
           SGG+  R LLA    LV    +  L+ DE  +G+     + I   L++L ++ + +L VT
Sbjct: 134 SGGQQQRVLLAR--ALVQDPDL--LLLDEPFAGVDPKTQEDIYELLRELRREGMTILVVT 189

Query: 488 H-APQVAARADRHFLVYKT 505
           H    V    DR  L+ +T
Sbjct: 190 HDLGLVLEYFDRVLLLNRT 208


>gnl|CDD|34219 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
           recombination, and repair].
          Length = 1041

 Score = 29.6 bits (66), Expect = 2.5
 Identities = 19/103 (18%), Positives = 35/103 (33%), Gaps = 4/103 (3%)

Query: 272 ENLSDAQHEIERSFSEIQYDAQELANIE--ERLFALRAM--SRKYSVSIDQLPELAKKME 327
           E L  A+  +ERSF++ Q        +E  ERL        +  +    +  P+L+   E
Sbjct: 573 EGLQTAEDLLERSFAQFQNSRSLPEIVEKLERLEKELNDIATELFGTDENDAPKLSLDYE 632

Query: 328 EDLADISEGNEKVVSLERVLYEARQAYDRVAQDISTKRYQFAK 370
           +    ++E      +  R L + R    +              
Sbjct: 633 KLRKKLNEEMRLQAAGLRALRKGRVVQIKDGLAALFWGRLLKL 675


>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 = 29.3 bits (66), Expect = 2.5
 Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 18/78 (23%)

Query: 429 SGGELSRFLLAL------KIVLVDQGSIPTLVFDEVDSGIGGAVADAIGYRLKQLSKKIQ 482
           SGG+  R  +A       KI+L D+   PT     +DS  G  V +     L++L+K+  
Sbjct: 142 SGGQQQRVAIARALANDPKIILADE---PT---GNLDSETGKEVMEL----LRELNKEAG 191

Query: 483 --LLAVTHAPQVAARADR 498
             ++ VTH P++A  ADR
Sbjct: 192 TTIVVVTHDPELAEYADR 209


>gnl|CDD|73032 cd03273, ABC_SMC2_euk, Eukaryotic SMC2 proteins; SMC proteins are
           large (approximately 110 to 170 kDa), and each is
           arranged into five recognizable domains.  Amino-acid
           sequence homology of SMC proteins between species is
           largely confined to the amino- and carboxy-terminal
           globular domains.  The amino-terminal domain contains a
           'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the
           single-letter amino-acid code), which by mutational
           studies has been shown to be essential in several
           proteins.  The carboxy-terminal domain contains a
           sequence (the DA-box) that resembles a 'Walker B' motif,
           and a motif with homology to the signature sequence of
           the ATP-binding cassette (ABC) family of ATPases.  The
           sequence homology within the carboxy-terminal domain is
           relatively high within the SMC1-SMC4 group, whereas SMC5
           and SMC6 show some divergence in both of these
           sequences.  In eukaryotic cells, the proteins are found
           as heterodimers of SMC1 paired with SMC3, SMC2 with
           SMC4, and SMC5 with SMC6 (formerly known as Rad18)..
          Length = 251

 Score = 29.4 bits (66), Expect = 2.5
 Identities = 20/75 (26%), Positives = 33/75 (44%)

Query: 429 SGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIGGAVADAIGYRLKQLSKKIQLLAVTH 488
           SGG+ S   L+L + L+     P  + DEVD+ +  +    IG  +K   K  Q + V+ 
Sbjct: 168 SGGQRSLVALSLILALLLFKPAPMYILDEVDAALDLSHTQNIGRMIKTHFKGSQFIVVSL 227

Query: 489 APQVAARADRHFLVY 503
              +   A+  F   
Sbjct: 228 KEGMFNNANVLFRTR 242


>gnl|CDD|36147 KOG0929, KOG0929, KOG0929, Guanine nucleotide exchange factor
           [Intracellular trafficking, secretion, and vesicular
           transport].
          Length = 1514

 Score = 29.6 bits (66), Expect = 2.5
 Identities = 27/114 (23%), Positives = 47/114 (41%), Gaps = 5/114 (4%)

Query: 202 PGEENELVVMRSKILKQERIAVELSSIMDDFHKSSSPISVISSMLR--RLERKSTEVPDL 259
             E +    MRSK+L  E +   L +    F  +   I  I   L     +   + VP +
Sbjct: 284 SEESDTQSHMRSKLLSLELLKSILENSGSVFRSNEHFIDAIKQYLCLALSKNSVSNVPMV 343

Query: 260 LQKSISFLNEAQENL-SDAQHEIERSFSEIQYDAQEL--ANIEERLFALRAMSR 310
            + S +       N  +  + EIE  FSEI     E   ++ ++++  LR ++R
Sbjct: 344 FELSCTIFVSLLSNFRTHLKAEIEVFFSEIFLRILENNTSSFQQKMMVLRILTR 397


>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 = 29.4 bits (66), Expect = 3.0
 Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 5/71 (7%)

Query: 429 SGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIGGAVADAIGYRLKQLSKKIQLLAVTH 488
           SGG+  R  L L   L ++  +  L+ DE  S +       I   + +L K+  ++ VTH
Sbjct: 143 SGGQQQR--LCLARALANEPEV--LLLDEPTSALDPISTAKIEELIAELKKEYTIVIVTH 198

Query: 489 APQVAAR-ADR 498
             Q AAR ADR
Sbjct: 199 NMQQAARVADR 209


>gnl|CDD|114015 pfam05266, DUF724, Protein of unknown function (DUF724).  This
           family contains several uncharacterized proteins found
           in Arabidopsis thaliana and other plants. This region is
           often found associated with Agenet domains and may
           contain coiled-coil.
          Length = 190

 Score = 29.3 bits (66), Expect = 3.1
 Identities = 16/73 (21%), Positives = 36/73 (49%), Gaps = 6/73 (8%)

Query: 283 RSFSEIQ---YDAQELANIEERLFALRAMSRKYSVSIDQLPELAKKMEEDLADISEGNEK 339
           + FSE++   ++ Q L +   +L +L+    K    +++   L K++ E      E + +
Sbjct: 76  KCFSELEKHGFNVQALQSRLNKLLSLKDDQTK---KLEERKGLEKEIAEKEISRQELDSE 132

Query: 340 VVSLERVLYEARQ 352
           +  LER + E ++
Sbjct: 133 IAELERKILELQR 145


>gnl|CDD|109493 pfam00437, GSPII_E, Type II/IV secretion system protein.  This
           family contains both type II and type IV pathway
           secretion proteins from bacteria. VirB11 ATPase is a
           subunit of the Agrobacterium tumefaciens transfer DNA
           (T-DNA) transfer system, a type IV secretion pathway
           required for delivery of T-DNA and effector proteins to
           plant cells during infection.
          Length = 283

 Score = 29.2 bits (66), Expect = 3.1
 Identities = 12/21 (57%), Positives = 16/21 (76%)

Query: 22  GLSILSGDTGSGKSILLDALI 42
           G  ++SG TGSGK+ LL AL+
Sbjct: 140 GNILVSGGTGSGKTTLLYALL 160


>gnl|CDD|37755 KOG2544, KOG2544, KOG2544, Dihydropteroate
           synthase/7,
           8-dihydro-6-hydroxymethylpterin-
           pyrophosphokinase/Dihydroneopterin aldolase [Coenzyme
           transport and metabolism].
          Length = 711

 Score = 29.2 bits (65), Expect = 3.3
 Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 458 VDSGIGGAV-----ADAIGY--RLKQLSKKIQLLAVTHAPQVAARADRHFLVYKTNKPDD 510
           +D GIG A       D I +  ++++   K+ +  ++HAP +   + + FL   T  P+ 
Sbjct: 608 IDPGIGFAKTWKQNLDIIMHLPKIREEMAKVSI-NLSHAPILLGPSRKRFLGDITGDPEA 666

Query: 511 TQRIETYVAVLT 522
             R    VA +T
Sbjct: 667 KDRDAATVACVT 678


>gnl|CDD|35996 KOG0777, KOG0777, KOG0777, Geranylgeranyl pyrophosphate
           synthase/Polyprenyl synthetase [Coenzyme transport and
           metabolism].
          Length = 322

 Score = 29.3 bits (65), Expect = 3.3
 Identities = 23/114 (20%), Positives = 45/114 (39%), Gaps = 7/114 (6%)

Query: 172 LKKYQEQKSSSQDVEFLRFSIDELQALAVQPGEENELVVMRSKILKQERIAVELSSIMDD 231
            K+Y E KS ++D+   +FS   + AL  +   E  L ++R +    + I      I++D
Sbjct: 206 DKEYSENKSFAEDLTEGKFSFPIIHALKTKGQTEQVLRILRQRTSDID-IKKYCIQILED 264

Query: 232 FHKSSSPISVISSMLRRLERK------STEVPDLLQKSISFLNEAQENLSDAQH 279
               +   + ++ ++            +  +PDL     +  N   E L    H
Sbjct: 265 TGSFAYTRNFLNQLVAEARSMIKNDGENPYLPDLASHLDTATNLHDELLYIIDH 318


>gnl|CDD|39623 KOG4422, KOG4422, KOG4422, Uncharacterized conserved protein
           [Function unknown].
          Length = 625

 Score = 28.9 bits (64), Expect = 3.3
 Identities = 30/147 (20%), Positives = 54/147 (36%), Gaps = 13/147 (8%)

Query: 260 LQKSISFLNEAQENLSDAQHEIERSFSEI--QYDAQELANIEERLFALRAMSRKYSVS-- 315
           ++ S       +    D   +++     +   Y++  +   E   F       + S S  
Sbjct: 131 VKDSCILYERMRSENVDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFGEDSTSSW 190

Query: 316 -----IDQLPELAKKMEEDLADISEGNEKVVSLER---VLYEARQAYDRVAQDISTKRYQ 367
                 D L E   K +E ++ +  G  K  SLER   +  E R A  +V ++       
Sbjct: 191 KSGAVADLLFETLPKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIG 250

Query: 368 FAKML-EKNVMAEMPALKLENVCFTVN 393
            +     K ++AEM + K+    FT N
Sbjct: 251 ASSYSVGKKLVAEMISQKMTPNLFTFN 277


>gnl|CDD|144377 pfam00753, Lactamase_B, Metallo-beta-lactamase superfamily. 
          Length = 148

 Score = 28.8 bits (64), Expect = 3.5
 Identities = 10/32 (31%), Positives = 16/32 (50%)

Query: 458 VDSGIGGAVADAIGYRLKQLSKKIQLLAVTHA 489
           +D+G+G   A  +   L    K I  + +THA
Sbjct: 20  IDTGLGADDALLLLAALGLDPKDIDAIILTHA 51


>gnl|CDD|39384 KOG4182, KOG4182, KOG4182, Uncharacterized conserved protein
           [Function unknown].
          Length = 828

 Score = 29.1 bits (64), Expect = 3.8
 Identities = 42/240 (17%), Positives = 89/240 (37%), Gaps = 33/240 (13%)

Query: 173 KKYQEQKSSSQDVEFLRFSIDELQALAVQPGEENELVVMRSK--ILKQERIAVELSSIMD 230
           K + E+           F  D    L +   E    +  +S   + +  R A + +++  
Sbjct: 22  KAFHEEDGRDDSEAAEAFIRDLEAKLQIAIEEIGAALEEQSGGALARMPRAAKDSAALQA 81

Query: 231 DFHKSSSPISVISSMLRRLERKSTEVPDLLQKSISFLNEAQENLSDAQHEIERS------ 284
           D H+    ++ I   L   E +S +    L +    L+  ++ L  A+  ++ +      
Sbjct: 82  DAHRLQEKMAAILLELAAAEGESADCIAALAR----LDNKKQKLEAAKESLQDAAGLGNL 137

Query: 285 FSEIQ--YDAQELANIEERLFALRAMSRKYSVSIDQLPELA--KKMEEDLAD-------- 332
            +E++  +   +L    ++L AL    +K   + ++L E A  +K  ED  D        
Sbjct: 138 LAELEDGFARGDLKGAADKLAAL----QKCLHAQEELAEFAERQKQLEDFEDRLEALAQP 193

Query: 333 -----ISEGNEKVVSLERVLYEARQAYDRVAQDISTKRYQFAKMLEKNVMAEMPALKLEN 387
                 +EG        R ++     + ++       + +F K L ++   +  A KL N
Sbjct: 194 RLTDAFAEGKTDQAQDFRQIFIRIGRFKQLELQYRAVQKKFIKQLWEDFDEKQGANKLAN 253


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

 Score = 28.6 bits (64), Expect = 4.1
 Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 6/81 (7%)

Query: 429 SGGELSRFLLALKIVLVDQGSIPTLVFDEVDSGIGGAVADAIGYRLKQLSKK--IQLLAV 486
           SGGE  R L+A  +    Q + P L+ DE  S +  A    +   L+ L+++  + ++ V
Sbjct: 140 SGGERQRVLIARALA---QET-PILLLDEPTSHLDIAHQIEVLELLRDLNREKGLTVVMV 195

Query: 487 THAPQVAARADRHFLVYKTNK 507
            H   +AAR   H ++ K  K
Sbjct: 196 LHDLNLAARYADHLILLKDGK 216


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

 Score = 28.7 bits (64), Expect = 4.5
 Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 4/32 (12%)

Query: 23  LSILSGDTGSGKSILLDALILVTGGRGDGGLV 54
           L+ L G++G+GK+ LLD L     GR  GG +
Sbjct: 819 LTALMGESGAGKTTLLDVL----AGRKTGGYI 846


>gnl|CDD|145542 pfam02456, Adeno_IVa2, Adenovirus IVa2 protein.  IVa2 protein can
           interact with the adenoviral packaging signal and that
           this interaction involves DNA sequences that have
           previously been demonstrated to be required for
           packaging. During the course of lytic infection, the
           adenovirus major late promoter (MLP) is induced to high
           levels after replication of viral DNA has started. IVa2
           is a transcriptional activator of the major late
           promoter.
          Length = 370

 Score = 28.5 bits (64), Expect = 4.7
 Identities = 11/31 (35%), Positives = 17/31 (54%)

Query: 12  IESLDIDFSAGLSILSGDTGSGKSILLDALI 42
           + SL+      + ++ G TG GKS LL  L+
Sbjct: 78  LPSLNYGLQPVIGVVYGPTGCGKSQLLRNLL 108


>gnl|CDD|35737 KOG0517, KOG0517, KOG0517, Beta-spectrin [Cytoskeleton].
          Length = 2473

 Score = 28.4 bits (63), Expect = 5.0
 Identities = 28/130 (21%), Positives = 54/130 (41%), Gaps = 6/130 (4%)

Query: 218  QERIAVELSSIMDDFHKSSSPISVISSMLRRLERKSTEVPDLLQKSISFLNEAQENLSDA 277
             + +  E+ +  D+F   S+ I +  S+L R    S E+ + L+       E  E     
Sbjct: 1947 HQGLKAEIEAREDNF---SACIELGKSLLLRKHYASEEIKEKLRALQDRREELYEKWERR 2003

Query: 278  QHEIERSFSEIQYDAQELANIEERLFALRAM--SRKYSVSIDQLPELAKKMEEDLADISE 335
               +++     Q+ A++    E  L A      S +   S+D++ +L K+ E      + 
Sbjct: 2004 WEWLQQILEVHQF-ARDAKVAEAWLIAQEPYLRSSELGSSVDEVEKLIKRHEAFEKSAAA 2062

Query: 336  GNEKVVSLER 345
              E+  +LER
Sbjct: 2063 QEERFSALER 2072


>gnl|CDD|31303 COG1106, COG1106, Predicted ATPases [General function prediction
          only].
          Length = 371

 Score = 28.5 bits (63), Expect = 5.2
 Identities = 14/45 (31%), Positives = 23/45 (51%)

Query: 2  TRLSIYNIVLIESLDIDFSAGLSILSGDTGSGKSILLDALILVTG 46
              I N      L+++    ++I+ G  G+GKS LL+AL  + G
Sbjct: 3  KSFKIKNFKSFRELELEDFGKINIIYGANGAGKSNLLEALYFLKG 47


>gnl|CDD|29991 cd01125, repA, Hexameric Replicative Helicase RepA.  RepA is
          encoded by a plasmid, which is found in most Gram
          negative bacteria. RepA is a 5'-3' DNA helicase which
          can utilize ATP, GTP and CTP to a lesser extent..
          Length = 239

 Score = 28.4 bits (63), Expect = 6.0
 Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 23 LSILSGDTGSGKS-ILLDALILVTGGRGDGGLVRRHAEKGQVV 64
          +S L    G+GKS +LL   + +  G+   G   +  E G+VV
Sbjct: 3  VSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVV 45


>gnl|CDD|57925 cd01854, YjeQ_engC, YjeQ/EngC.  YjeQ (YloQ in Bacillus subtilis)
           represents a protein family whose members are broadly
           conserved in bacteria and have been shown to be
           essential to the growth of E. coli and B. subtilis.
           Proteins of the YjeQ family contain all sequence motifs
           typical of the vast class of P-loop-containing GTPases,
           but show a circular permutation, with a G4-G1-G3 pattern
           of motifs as opposed to the regular G1-G3-G4 pattern
           seen in most GTPases. All YjeQ family proteins display a
           unique domain architecture, which includes an N-terminal
           OB-fold RNA-binding domain, the central permuted GTPase
           domain, and a zinc knuckle-like C-terminal cysteine
           domain. This domain architecture suggests a role for
           YjeQ as a regulator of translation..
          Length = 287

 Score = 28.2 bits (63), Expect = 6.4
 Identities = 11/31 (35%), Positives = 18/31 (58%)

Query: 12  IESLDIDFSAGLSILSGDTGSGKSILLDALI 42
           ++ L        S+L G +G GKS L++AL+
Sbjct: 152 LDELREYLKGKTSVLVGQSGVGKSTLINALL 182


>gnl|CDD|143401 cd07082, ALDH_F11_NP-GAPDH, NADP+-dependent non-phosphorylating
           glyceraldehyde 3-phosphate dehydrogenase and ALDH family
           11.  NADP+-dependent non-phosphorylating glyceraldehyde
           3-phosphate dehydrogenase (NP-GAPDH, EC=1.2.1.9)
           catalyzes the irreversible oxidation of glyceraldehyde
           3-phosphate to 3-phosphoglycerate generating NADPH for
           biosynthetic reactions.  This CD also includes the
           Arabidopsis thaliana osmotic-stress-inducible ALDH
           family 11, ALDH11A3  and similar sequences. In
           autotrophic eukaryotes, NP-GAPDH generates NADPH for
           biosynthetic processes from photosynthetic
           glyceraldehyde-3-phosphate exported from the chloroplast
           and catalyzes one of the classic glycolytic bypass
           reactions unique to plants.
          Length = 473

 Score = 27.9 bits (63), Expect = 6.9
 Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 6/61 (9%)

Query: 239 ISVISSMLRRLERKSTEVPDLLQKSISFLNEAQENLSDAQHEIERSFSEIQYDAQELANI 298
           I  +      L+    EV +LL        E  + L DA  E++R+   I+   +EL  +
Sbjct: 64  IDCLHKFADLLKENKEEVANLLMW------EIGKTLKDALKEVDRTIDYIRDTIEELKRL 117

Query: 299 E 299
           +
Sbjct: 118 D 118


>gnl|CDD|36213 KOG0995, KOG0995, KOG0995, Centromere-associated protein HEC1 [Cell
           cycle control, cell division, chromosome partitioning].
          Length = 581

 Score = 28.0 bits (62), Expect = 7.1
 Identities = 16/83 (19%), Positives = 35/83 (42%)

Query: 260 LQKSISFLNEAQENLSDAQHEIERSFSEIQYDAQELANIEERLFALRAMSRKYSVSIDQL 319
           L+K  + +    E+L     E+E   +E + D  +  ++ E+   L+    K+   + Q+
Sbjct: 226 LEKYFTSIANEIEDLKKTNRELEEMINEREKDPGKEESLREKKARLQDDVNKFQAYVSQM 285

Query: 320 PELAKKMEEDLADISEGNEKVVS 342
               + ME+ L  +    E+   
Sbjct: 286 KSKKQHMEKKLEMLKSEIEEKEE 308


>gnl|CDD|72991 cd03232, ABC_PDR_domain2, The pleiotropic drug resistance-like
          (PDR) family of ATP-binding cassette (ABC)
          transporters. PDR is a well-described phenomenon
          occurring in fungi and shares several similarities with
          processes in bacteria and higher eukaryotes.  This PDR
          subfamily represents domain I of its (ABC-IM)2
          organization.  ABC transporters are a large family of
          proteins involved in the transport of a wide variety of
          different compounds including sugars, ions, peptides,
          and more complex organic molecules.  The nucleotide
          binding domain shows the highest similarity between all
          members of the family.  ABC transporters are a subset
          of nucleotide hydrolases that contain a signature
          motif, Q-loop, and H-loop/switch region, in addition
          to, the Walker A motif/P-loop and Walker B motif
          commonly found in a number of ATP- and GTP-binding and
          hydrolyzing proteins..
          Length = 192

 Score = 27.8 bits (62), Expect = 8.3
 Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 4/33 (12%)

Query: 23 LSILSGDTGSGKSILLDALILVTGGRGDGGLVR 55
          L+ L G++G+GK+ LLD L     GR   G++ 
Sbjct: 35 LTALMGESGAGKTTLLDVL----AGRKTAGVIT 63


>gnl|CDD|185749 cd09236, V_AnPalA_UmRIM20_like, Protein-interacting V-domains of
           Aspergillus nidulans PalA/RIM20, Ustilago maydis RIM20,
           and related proteins.  This family belongs to the
           V_Alix_like superfamily which includes the V-shaped (V)
           domains of Bro1 and Rim20 from Saccharomyces cerevisiae,
           mammalian Alix (apoptosis-linked gene-2 interacting
           protein X), His-Domain type N23 protein tyrosine
           phosphatase (HD-PTP, also known as PTPN23), and related
           domains. Aspergillus nidulas PalA/RIM20 and Ustilago
           maydis RIM20, like Saccharomyces cerevisiae Rim20,
           participate in the response to the external pH via the
           Pal/Rim101 pathway; however, Saccharomyces cerevisiae
           Rim20 does not belong to this family. This pathway is a
           signaling cascade resulting in the activation of the
           transcription factor PacC/Rim101. The mammalian Alix
           V-domain (belonging to a different family) contains a
           binding site, partially conserved in the superfamily,
           for the retroviral late assembly (L) domain YPXnL motif.
           Aspergillus nidulas PalA binds a nonviral YPXnL motif
           (tandem YPXL/I motifs within PacC). The Alix V-domain is
           also a dimerization domain. In addition to this
           V-domain, members of the V_Alix_like superfamily also
           have an N-terminal Bro1-like domain, which has been
           shown to bind CHMP4/Snf7, a component of the ESCRT-III
           complex.
          Length = 353

 Score = 27.7 bits (62), Expect = 8.3
 Identities = 42/158 (26%), Positives = 67/158 (42%), Gaps = 15/158 (9%)

Query: 192 IDELQALAVQPGEENELVVMRSKILKQERIAVELSS---IMDDFHKSSSPISVISSM--- 245
             E +    Q G  +ELV  R K+ + E +   L+     +++F  SS   S+   +   
Sbjct: 136 AAEYEGYLKQAGASDELV--RRKLDEWEDLIQILTGDERDLENFVPSSRRPSIPPELERH 193

Query: 246 LRRLERKSTEVPDLLQKSISFLNEAQENLS--DAQHEIERSFS--EIQYDAQELANIE-E 300
           +R L     E+  L  +    +  A+      D + EI R  +  E +Y A E+A    E
Sbjct: 194 VRALRVSLEELDRLESRRRRKVERARTKARADDIRPEILREAARLEREYPATEVAPAHFE 253

Query: 301 RLFALRAMSRKYSVSIDQLPELAKKMEEDLADISEGNE 338
            LF  R    KY   +D + E A++ EE L  I   N+
Sbjct: 254 DLFDKRL--AKYDKDLDAVSEEAQEQEEILQQIEVANK 289


>gnl|CDD|36247 KOG1029, KOG1029, KOG1029, Endocytic adaptor protein intersectin
           [Signal transduction mechanisms, Intracellular
           trafficking, secretion, and vesicular transport].
          Length = 1118

 Score = 27.8 bits (61), Expect = 8.5
 Identities = 32/179 (17%), Positives = 67/179 (37%), Gaps = 18/179 (10%)

Query: 214 KILKQERIAVELSSIMDDFHKSSSPISVISSMLRRLERKSTEVPDLLQKSISFLNEAQEN 273
           K L  E +     S      +S++ IS +      +     E P  L   ++F ++ +EN
Sbjct: 269 KTLPPELVPPSFRSS-----RSANSISGLEP--GGVGVVDAEPPKKLPAPVTFEDKRKEN 321

Query: 274 LSDAQHEIERS----FSEIQYDAQELANIEERLFALRAMSRKYSVSIDQLPELAKKMEED 329
               Q E+ER       + Q + +E+   E      +   R+      QL EL K++E  
Sbjct: 322 YEKGQAELERRRQALEEQQQREREEVEQKEREEEEKKERERQEQERKAQL-ELEKQLERQ 380

Query: 330 LADISEGNEKVVSLERVLYEARQAYDRVAQDISTKRYQFAKMLEKNVMAEMPALKLENV 388
                +  E+     +   E R+A     +    ++ ++ +   + ++ +    +   V
Sbjct: 381 REIERQREEE----RKKEIERREAARE--ELEKQRQLEWERARRQEMLNQKNREQEWIV 433


>gnl|CDD|34945 COG5383, COG5383, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 295

 Score = 27.7 bits (61), Expect = 8.8
 Identities = 29/126 (23%), Positives = 41/126 (32%), Gaps = 7/126 (5%)

Query: 244 SMLRRLERKSTEVP----DLLQKSISFLNEAQENLSDAQHEIERSFSEIQYDAQELANIE 299
           SMLRRL       P    DL    +   + A E +S A  + ER      + A+    IE
Sbjct: 76  SMLRRLFAVMGMYPVGYYDLSTAGVPVHSTAFEPVSFADEDGERHPG--VHTARFGE-IE 132

Query: 300 ERLFALRAMSRKYSVSIDQLPELAKKMEEDLADISEGNEKVVSLERVLYEARQAYDRVAQ 359
           +R  AL    R     + Q            A   E  E+       + E   A  R   
Sbjct: 133 QRGVALTPKGRVLYDDLLQAASTGFNAMAYSATAREIFEQFPDSMSEMREQGLAQFRYLL 192

Query: 360 DISTKR 365
           ++    
Sbjct: 193 ELVAAA 198


>gnl|CDD|32466 COG2312, COG2312, Erythromycin esterase homolog [General function
           prediction only].
          Length = 405

 Score = 27.6 bits (61), Expect = 9.0
 Identities = 35/166 (21%), Positives = 49/166 (29%), Gaps = 25/166 (15%)

Query: 404 DGIDRVEFYVQTNRGENPGPLMKLASGGELSRFLLALKIVLVDQGSIPTLVFDEV--DSG 461
               +V FY            M+  S   L  +L  +      +     +    +  D G
Sbjct: 135 SAGPQVGFY-------GFDAQMENGSAAALRAYLDTVDPRAAARARARPVCAATLGTDPG 187

Query: 462 IGGAVADAIGYRLKQLSKKIQLLAVTHAPQVAARADRHFLV------YKTNKPD------ 509
              A A+      KQ S+ I  L   H  +  A A     +           PD      
Sbjct: 188 QDDAFAEKAAALDKQASEAINAL-DEHRQERRALAQELARLVEQAERRYREMPDAGDASW 246

Query: 510 ---DTQRIETYVAVLTPQERREEIARMLAGSHITEEARAAAEILLE 552
              D    ET  AVL      ++I      SHI +     AE L E
Sbjct: 247 NLRDAAMAETLEAVLATDYPPDKIIVWAHNSHIRKARHLLAEALRE 292


>gnl|CDD|73184 cd00186, TOP1Ac, DNA Topoisomerase, subtype IA; DNA-binding,
           ATP-binding and catalytic domain of bacterial DNA
           topoisomerases I and III, and eukaryotic DNA
           topoisomerase III and eubacterial and archael reverse
           gyrases. Topoisomerases clevage single or double
           stranded DNA and then rejoin the broken phosphodiester
           backbone. Proposed catalytic mechanism of single
           stranded DNA cleavage is by phosphoryl transfer through
           a tyrosine nucleophile using acid/base catalysis. Tyr is
           activated by a nearby group (not yet identified) acting
           as a general base for nucleophilic attack on the 5'
           phosphate of the scissile bond. Arg and Lys stabilize
           the pentavalent transition state. Glu then acts as a
           proton donor for the leaving 3'-oxygen, upon cleavage of
           the scissile strand..
          Length = 381

 Score = 27.5 bits (61), Expect = 10.0
 Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 3/38 (7%)

Query: 320 PELAKKMEEDLADISEGNEKVVSLERVLYEARQAYDRV 357
           PE   K+EE L +I+EG +     + VL E  + + ++
Sbjct: 346 PEFTAKLEEKLDEIAEGKK---DYQEVLEEFYEEFKKI 380


  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
   0.318    0.134    0.362 

Gapped
Lambda     K      H
   0.267   0.0643    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 6,253,670
Number of extensions: 337586
Number of successful extensions: 1442
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1420
Number of HSP's successfully gapped: 197
Length of query: 554
Length of database: 6,263,737
Length adjustment: 99
Effective length of query: 455
Effective length of database: 4,124,446
Effective search space: 1876622930
Effective search space used: 1876622930
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 (21.7 bits)
S2: 60 (27.1 bits)