RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780711|ref|YP_003065124.1| signal recognition particle
protein [Candidatus Liberibacter asiaticus str. psy62]
         (461 letters)



>gnl|CDD|30887 COG0541, Ffh, Signal recognition particle GTPase [Intracellular
           trafficking and secretion].
          Length = 451

 Score =  546 bits (1408), Expect = e-156
 Identities = 232/459 (50%), Positives = 317/459 (69%), Gaps = 9/459 (1%)

Query: 1   MFDNLQERLGSIFQNITGKGSLSETDISNTLREIRRTFLEADVSLEVVQSFSKRVQEKAK 60
           MF++L +RL +  + + GKG ++E D+   LREIRR  LEADV+L+VV+ F KR++E+A 
Sbjct: 1   MFESLSDRLSNALKKLRGKGRITEKDVKEALREIRRALLEADVNLKVVKDFIKRIKERAL 60

Query: 61  GEKILRSIQPGQMVIKIVHDELVEVLGKESIELDLNAPSPLVIMLVGLQGSGKTTTTAKI 120
           GE++ + + PGQ  IKIV++ELV++LG E+ EL+L    P VI++VGLQGSGKTTT  K+
Sbjct: 61  GEEVPKGLTPGQQFIKIVYEELVKLLGGENSELNLAKKPPTVILMVGLQGSGKTTTAGKL 120

Query: 121 AYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDTLEVIPEQSPEKIAIRATQSAR 180
           A +LK  K KK+L+ + D +RPAA EQL+ L EQ+ V       E+ P +IA  A + A+
Sbjct: 121 AKYLKK-KGKKVLLVAADTYRPAAIEQLKQLAEQVGVPFFGSGTEKDPVEIAKAALEKAK 179

Query: 181 DGGYDAVILDTAGRNHINDSLMQEISEIKSLTNPHEILLVADALTGQDAVHLARNFDKIV 240
           + GYD VI+DTAGR HI++ LM E+ EIK + NP E LLV DA+ GQDAV+ A+ F++ +
Sbjct: 180 EEGYDVVIVDTAGRLHIDEELMDELKEIKEVINPDETLLVVDAMIGQDAVNTAKAFNEAL 239

Query: 241 DLTGIILTRMDGDGRGGAALSMRTVTGKPIKAIGTGEKINDLENFFPDRIANRILGMGDV 300
            +TG+ILT++DGD RGGAALS R +TGKPIK IGTGEKI+DLE F PDR A+RILGMGDV
Sbjct: 240 GITGVILTKLDGDARGGAALSARAITGKPIKFIGTGEKIDDLEPFHPDRFASRILGMGDV 299

Query: 301 VSLVEKAARNLNEKQAALTAKKIAKGKFDLEDLAEQFRQTQKIGGIGSILRMLPGMPSLK 360
           +SL+EKA   ++E++A   A+K+ KGKF LED  EQ  Q +K+G +  +L M+PGM  +K
Sbjct: 300 LSLIEKAEEVVDEEEAEKLAEKLKKGKFTLEDFLEQLEQMKKMGPLSKLLSMIPGM-GMK 358

Query: 361 QNIMPSSFDDKTINHHIAIIASMTKEERANPSIIKHSRKKRIAAGSGTNAAKINKLLKLH 420
            +      D+K +    AII SMT EER NP II  SRK+RIA GSGT+   +NKLLK  
Sbjct: 359 DSDKDIELDEKKLKRIEAIIDSMTPEERENPDIINASRKRRIARGSGTSVQDVNKLLKQF 418

Query: 421 RQVAEMMHSTQGLGGNALTQQIMGRLKSKIGFGKNGRFP 459
           +Q+ +MM    G GG        G++   +     G+FP
Sbjct: 419 KQMKKMMKKMSGGGG-------KGKMMRGMKGMMGGKFP 450


>gnl|CDD|35999 KOG0780, KOG0780, KOG0780, Signal recognition particle, subunit
           Srp54 [Intracellular trafficking, secretion, and
           vesicular transport].
          Length = 483

 Score =  314 bits (805), Expect = 5e-86
 Identities = 156/457 (34%), Positives = 238/457 (52%), Gaps = 8/457 (1%)

Query: 1   MFDNLQERLGSIFQNITGKGSLSETDISNTLREIRRTFLEADVSLEVVQSFSKRVQEKAK 60
           +   L  R+ S F  ++   S+ ET ++  L+EI R  LE+DV+  +V+   + +++   
Sbjct: 2   VLAELGRRITSAFSRMSNATSIDETALNTMLKEICRALLESDVNPRLVKELRENIRKIIN 61

Query: 61  GEKILRSIQPGQMVIKIVHDELVEVLGKESIELDLNAPSPLVIMLVGLQGSGKTTTTAKI 120
            EK+   +   +++ K V DELV++L      L      P VIM VGLQGSGKTTT  K+
Sbjct: 62  LEKLASGVNKRRIIQKAVFDELVKLLDPGKSALQPKKGKPSVIMFVGLQGSGKTTTCTKL 121

Query: 121 AYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDTLEVIPEQSPEKIAIRATQSAR 180
           AY+ K  K  K+ +   D  R  A +QL+    + +V       E  P KIA       +
Sbjct: 122 AYYYKK-KGYKVALVCADTFRAGAFDQLKQNATKARVPFYGSYTEADPVKIASEGVDRFK 180

Query: 181 DGGYDAVILDTAGRNHINDSLMQEISEIKSLTNPHEILLVADALTGQDAVHLARNFDKIV 240
              +D +I+DT+GR+    SL +E+ ++     P EI+ V DA  GQ A   AR F + V
Sbjct: 181 KENFDVIIVDTSGRHKQEASLFEEMKQVSKAIKPDEIIFVMDASIGQAAEAQARAFKETV 240

Query: 241 DLTGIILTRMDGDGRGGAALSMRTVTGKPIKAIGTGEKINDLENFFPDRIANRILGMGDV 300
           D+  +ILT++DG  +GG ALS    T  PI  IGTGE ++DLE F P    +R+LGMGD+
Sbjct: 241 DVGAVILTKLDGHAKGGGALSAVAATKSPIIFIGTGEHMDDLEPFDPKPFVSRLLGMGDI 300

Query: 301 VSLVEKAARNLNEKQAALTAKKIAKGKFDLEDLAEQFRQTQKIGGIGSILRMLPGMPSL- 359
             LVEK      +    L  +K+ +GKF L D  +QF+   K+G +  +L M+PGM  + 
Sbjct: 301 EGLVEKVQEVGKDDAKELV-EKLKQGKFTLRDFYDQFQNIMKMGPLSQVLGMIPGMSMMS 359

Query: 360 KQNIMPSSFDDKTINHHIAIIASMTKEERANPSII--KHSRKKRIAAGSGTNAAKINKLL 417
           K N   SS     +   + ++ SMT EE  +P +   + SR  R+A GSGT+  ++ +LL
Sbjct: 360 KGNEEESS---AKLKRMMTMMDSMTDEELDSPELFVEEPSRIMRVARGSGTSVQEVMELL 416

Query: 418 KLHRQVAEMMHSTQGLGGNALTQQIMGRLKSKIGFGK 454
             +++ A MM    G+ G         +  +     K
Sbjct: 417 AQYKKFAAMMKKIGGIKGIFGALGNPNKNMNPAPMAK 453


>gnl|CDD|144151 pfam00448, SRP54, SRP54-type protein, GTPase domain.  This family
           includes relatives of the G-domain of the SRP54 family
           of proteins.
          Length = 196

 Score =  250 bits (641), Expect = 6e-67
 Identities = 99/197 (50%), Positives = 136/197 (69%), Gaps = 1/197 (0%)

Query: 100 PLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDT 159
           P VI+LVGLQGSGKTTT AK+A +LK  + KK+L+ + D  R AA EQL+ L E++ V  
Sbjct: 1   PNVILLVGLQGSGKTTTIAKLAAYLK-KQGKKVLLVAADTFRAAAIEQLKQLAERLGVPV 59

Query: 160 LEVIPEQSPEKIAIRATQSARDGGYDAVILDTAGRNHINDSLMQEISEIKSLTNPHEILL 219
                   P  +A  A + A+   YD V++DTAGR   + +LM E+ +IK +  P E+LL
Sbjct: 60  FGSGTGSDPAAVAFDAVEKAKAENYDVVLVDTAGRLQNDKNLMDELKKIKRVIAPDEVLL 119

Query: 220 VADALTGQDAVHLARNFDKIVDLTGIILTRMDGDGRGGAALSMRTVTGKPIKAIGTGEKI 279
           V DA TGQ+A++ A+ F++ V +TG+ILT++DGD +GGAALS+   TGKPIK IG GEKI
Sbjct: 120 VLDATTGQNALNQAKAFNEAVGITGVILTKLDGDAKGGAALSIAAETGKPIKFIGVGEKI 179

Query: 280 NDLENFFPDRIANRILG 296
           +DLE F P+R  +R+LG
Sbjct: 180 DDLEPFDPERFVSRLLG 196


>gnl|CDD|48379 cd03115, SRP, The signal recognition particle (SRP) mediates the
           transport to or across the plasma membrane in bacteria
           and the endoplasmic reticulum in eukaryotes. SRP
           recognizes N-terminal sighnal sequences of newly
           synthesized polypeptides at the ribosome. The
           SRP-polypeptide complex is then targeted to the membrane
           by an interaction between SRP and its cognated receptor
           (SR). In mammals, SRP consists of six protein subunits
           and a 7SL RNA. One of these subunits is a 54 kd protein
           (SRP54), which is a GTP-binding protein that interacts
           with the signal sequence when it emerges from the
           ribosome. SRP54 is a multidomain protein that consists
           of an N-terminal domain, followed by a central G
           (GTPase) domain and a C-terminal M domain..
          Length = 173

 Score =  226 bits (577), Expect = 1e-59
 Identities = 98/173 (56%), Positives = 130/173 (75%), Gaps = 1/173 (0%)

Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDTLE 161
           VI+LVGLQG GKTTT AK+A +LK  K KK+L+ + D +RPAA EQLR LGEQ+ V   E
Sbjct: 2   VILLVGLQGVGKTTTAAKLALYLKK-KGKKVLLVAADTYRPAAIEQLRVLGEQVGVPVFE 60

Query: 162 VIPEQSPEKIAIRATQSARDGGYDAVILDTAGRNHINDSLMQEISEIKSLTNPHEILLVA 221
               + P  IA RA + AR+  +D VI+DTAGR  I+++LM+E+ +IK +  P E+LLV 
Sbjct: 61  EGEGKDPVSIAKRAIEHAREENFDVVIVDTAGRLQIDENLMEELKKIKRVVKPDEVLLVV 120

Query: 222 DALTGQDAVHLARNFDKIVDLTGIILTRMDGDGRGGAALSMRTVTGKPIKAIG 274
           DA+TGQDAV+ A+ F++ + +TG+ILT++DGD RGGAALS+R VTGKPIK IG
Sbjct: 121 DAMTGQDAVNQAKAFNEALGITGVILTKLDGDARGGAALSIRAVTGKPIKFIG 173


>gnl|CDD|30898 COG0552, FtsY, Signal recognition particle GTPase [Intracellular
           trafficking and secretion].
          Length = 340

 Score =  212 bits (542), Expect = 1e-55
 Identities = 107/312 (34%), Positives = 162/312 (51%), Gaps = 20/312 (6%)

Query: 1   MFDNLQERLGSIFQNITGK------GSLSETDISNTLREIRRTFLEADVSLEVVQSFSKR 54
            F+ L++ L    +N            + E    + L E+    +EADV +E  +   + 
Sbjct: 33  WFERLKQGLSKTKKNFGKGIKGLFLKKIKEKLDEDLLEELEELLIEADVGVETAEEIIEE 92

Query: 55  VQEKAKGEKILRSIQPGQMVIKIVHDELVEVLGK----ESIELDLNAPSPLVIMLVGLQG 110
           ++   K E   + I+  + V + + + L+E+L      +          P VI+ VG+ G
Sbjct: 93  LR---KREGKKKKIKDEETVKEALREALIEILRPVDKVDLPLEIPKEKKPFVILFVGVNG 149

Query: 111 SGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDTLEVIPEQSPEK 170
            GKTTT AK+A +LK  + K +L+A+ D  R AA EQL   GE++ V  +       P  
Sbjct: 150 VGKTTTIAKLAKYLKQ-QGKSVLLAAGDTFRAAAIEQLEVWGERLGVPVISGKEGADPAA 208

Query: 171 IAIRATQSARDGGYDAVILDTAGRNHINDSLMQEISEIKSLTN------PHEILLVADAL 224
           +A  A Q+A+  G D V++DTAGR H   +LM E+ +I  +        PHEILLV DA 
Sbjct: 209 VAFDAIQAAKARGIDVVLIDTAGRLHNKKNLMDELKKIVRVIKKDDPDAPHEILLVLDAT 268

Query: 225 TGQDAVHLARNFDKIVDLTGIILTRMDGDGRGGAALSMRTVTGKPIKAIGTGEKINDLEN 284
           TGQ+A+  A+ F++ V L GIILT++DG  +GG  LS+    G PIK IG GE  +DL  
Sbjct: 269 TGQNALSQAKIFNEAVGLDGIILTKLDGTAKGGIILSIAYELGIPIKFIGVGEGYDDLRP 328

Query: 285 FFPDRIANRILG 296
           F  +   + +LG
Sbjct: 329 FDAEWFVDALLG 340


>gnl|CDD|36000 KOG0781, KOG0781, KOG0781, Signal recognition particle receptor,
           alpha subunit [Intracellular trafficking, secretion, and
           vesicular transport].
          Length = 587

 Score =  145 bits (368), Expect = 2e-35
 Identities = 94/306 (30%), Positives = 158/306 (51%), Gaps = 22/306 (7%)

Query: 11  SIFQNITGKGSLSETDISNTLREIRRTFLEADVSLEVVQSFSKRVQEKAKGEKILRSIQP 70
            +F+ + G  SLSE D++  L ++    +  +V+ E+ +   + V    +G+K+      
Sbjct: 282 GLFKGLVGSKSLSEEDLNPVLDKMTEHLITKNVAAEIAEKLCESVAASLEGKKVGSFSTV 341

Query: 71  GQMVIKIVHDELVEVLG-KESIEL--DLNAPS----PLVIMLVGLQGSGKTTTTAKIAYH 123
              V + + D LV++L  + S++L  D+ +      P VI  VG+ G GK+T  AKIAY 
Sbjct: 342 ESTVKEALRDALVQILTPQRSVDLLRDIMSARRRKRPYVISFVGVNGVGKSTNLAKIAYW 401

Query: 124 LKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDTLEVIP------EQSPEKIAIRATQ 177
           L    K ++L+A+ D  R  A EQLR   E++      ++        +    +A  A Q
Sbjct: 402 L-LQNKFRVLIAACDTFRSGAVEQLRTHVERLSALHGTMVELFEKGYGKDAAGVAKEAIQ 460

Query: 178 SARDGGYDAVILDTAGRNHINDSLMQEISEIKSLTNPHEILLVADALTGQDAVHLARNFD 237
            AR+ G+D V++DTAGR H N  LM  ++++  +  P  IL V +AL G D+V   + F+
Sbjct: 461 EARNQGFDVVLIDTAGRMHNNAPLMTSLAKLIKVNKPDLILFVGEALVGNDSVDQLKKFN 520

Query: 238 KIV-------DLTGIILTRMDG-DGRGGAALSMRTVTGKPIKAIGTGEKINDLENFFPDR 289
           + +        + GI+LT+ D  D + GAA+SM  +TGKPI  +G G+  +DL       
Sbjct: 521 RALADHSTPRLIDGILLTKFDTVDDKVGAAVSMVYITGKPILFVGVGQTYSDLRKLNVKA 580

Query: 290 IANRIL 295
           +   ++
Sbjct: 581 VVATLM 586


>gnl|CDD|145891 pfam02978, SRP_SPB, Signal peptide binding domain. 
          Length = 100

 Score =  127 bits (321), Expect = 8e-30
 Identities = 47/101 (46%), Positives = 65/101 (64%), Gaps = 1/101 (0%)

Query: 327 KFDLEDLAEQFRQTQKIGGIGSILRMLPGMPSLKQNIMPSSFDDKTINHHIAIIASMTKE 386
           KF L D  EQ +Q +K+G +  +L M+PGM  L + +     D+K +    AII SMT +
Sbjct: 1   KFTLRDFLEQLQQIKKMGPLSKLLSMIPGMGKLPK-LAEQELDEKKLKRIEAIIDSMTPK 59

Query: 387 ERANPSIIKHSRKKRIAAGSGTNAAKINKLLKLHRQVAEMM 427
           ER NP II  SRK+RIA GSGT+  ++NKLLK  +Q+ +MM
Sbjct: 60  ERDNPEIINGSRKRRIAKGSGTSVQEVNKLLKQFKQMKKMM 100


>gnl|CDD|31609 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
           secretion].
          Length = 407

 Score = 95.8 bits (238), Expect = 2e-20
 Identities = 65/212 (30%), Positives = 108/212 (50%), Gaps = 10/212 (4%)

Query: 88  KESIELDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTL-KKKKILMASLDVHRPAAQE 146
             S+  +L      VI LVG  G GKTTT AK+A     L KKKK+ + + D +R  A E
Sbjct: 191 LLSLIENLIVEQKRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVE 250

Query: 147 QLRYLGEQIQVDTLEVIPEQSPEKIAIRATQSARDGGYDAVILDTAGRNHINDSLMQEIS 206
           QL+   + + V  LEV+   SP+++A            D +++DTAGR+  +   ++E+ 
Sbjct: 251 QLKTYADIMGVP-LEVV--YSPKELAEAIEALRD---CDVILVDTAGRSQYDKEKIEELK 304

Query: 207 EIKSLTNPHEILLVADALT-GQDAVHLARNFDKIVDLTGIILTRMDGDGRGGAALSMRTV 265
           E+  +++  E+ LV  A T  +D   + + F  +  + G+I T++D     G   S+   
Sbjct: 305 ELIDVSHSIEVYLVLSATTKYEDLKEIIKQF-SLFPIDGLIFTKLDETTSLGNLFSLMYE 363

Query: 266 TGKPIKAIGTGEKI-NDLENFFPDRIANRILG 296
           T  P+  +  G+++  D+    PD +  RILG
Sbjct: 364 TRLPVSYVTNGQRVPEDIVVANPDYLVRRILG 395


>gnl|CDD|145830 pfam02881, SRP54_N, SRP54-type protein, helical bundle domain. 
          Length = 77

 Score = 57.2 bits (139), Expect = 8e-09
 Identities = 21/81 (25%), Positives = 35/81 (43%), Gaps = 7/81 (8%)

Query: 5  LQERLGSIFQNITGKGS---LSETDISNTLREIRRTFLEADVSLEVVQSFSKRVQEKAKG 61
          L+E L      + GK     L E  I   L E+    LEADV +E  +   +R++E    
Sbjct: 1  LKEGLSKTRSKLGGKIKDLFLGEKKIDELLEELEEALLEADVGVETTEKIIERLKELVGR 60

Query: 62 EKILRSIQPGQMVIKIVHDEL 82
              + +   + + K + +EL
Sbjct: 61 ----KGLSDPEEIKKALKEEL 77


>gnl|CDD|73298 cd02035, ArsA, ArsA ATPase functionas as an efflux pump located on
           the inner membrane of the cell. This ATP-driven oxyanion
           pump catalyzes the extrusion of arsenite, antimonite and
           arsenate. Maintenance of a low intracellular
           concentration of oxyanion produces resistance to the
           toxic agents. The pump is composed of two subunits, the
           catalytic ArsA subunit and the membrane subunit ArsB,
           which are encoded by arsA and arsB genes respectively.
           Arsenic efflux in bacteria is catalyzed by either ArsB
           alone or by ArsAB complex. The ATP-coupled pump,
           however, is more efficient. ArsA is composed of two
           homologous halves, A1 and A2, connected by a short
           linker sequence..
          Length = 217

 Score = 38.7 bits (90), Expect = 0.003
 Identities = 36/154 (23%), Positives = 55/154 (35%), Gaps = 40/154 (25%)

Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDTLE 161
           VI   G  G GKTT  A  A  L   + KK+L+ S D     + + L  L +   V+  E
Sbjct: 1   VIFFTGKGGVGKTTIAAATAVRL-AEEGKKVLLVSTDPAHNLSDKGLPNLSDAFIVEDPE 59

Query: 162 VIPEQSPEKIA--------------------------------IRATQSARDGGYDAVIL 189
           + P    E++                                 +   +   +G YD ++ 
Sbjct: 60  IAPNLYREEVDATRRVERAWGGEGGLMLELAAALPGIEELASLLAVFREFSEGLYDVIVF 119

Query: 190 DTAGRNHINDSLMQEISEIKSLTNPHE--ILLVA 221
           DTA   H    L++E+     LT+P      LV 
Sbjct: 120 DTAPTGHTLRLLVREL-----LTDPERTSFRLVT 148


>gnl|CDD|38089 KOG2878, KOG2878, KOG2878, Predicted kinase [General function
           prediction only].
          Length = 282

 Score = 38.9 bits (90), Expect = 0.003
 Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 2/52 (3%)

Query: 100 PLVIMLVGLQGSGKTTTTAKIAYHL--KTLKKKKILMASLDVHRPAAQEQLR 149
           PLVI   G QGSGK+T    + Y L  K +++      S+D      + Q  
Sbjct: 31  PLVIGFSGPQGSGKSTLVFALDYKLTKKYIQEYSSATISVDDFYLTHEGQAE 82


>gnl|CDD|33963 COG4240, COG4240, Predicted kinase [General function prediction
           only].
          Length = 300

 Score = 38.4 bits (89), Expect = 0.004
 Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 7/73 (9%)

Query: 69  QPGQMVIKIVHDELVEVLGK---ESIELDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLK 125
           +       +  D  + +L K    + E       PL++ + G QGSGK+T +A I   L 
Sbjct: 20  RLPPAFAALAQDLHLPLLAKIAPWAQERG----RPLIVGISGPQGSGKSTLSALIVRLLA 75

Query: 126 TLKKKKILMASLD 138
               ++    SLD
Sbjct: 76  AKGLERTATLSLD 88


>gnl|CDD|73290 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety of
           proteins which share a common ATP-binding domain.
           Functionally, proteins in this superfamily use the
           energy from hydrolysis of NTP to transfer electron or
           ion..
          Length = 99

 Score = 36.2 bits (83), Expect = 0.017
 Identities = 13/33 (39%), Positives = 19/33 (57%)

Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILM 134
           VI++ G  G GKTT  A +A  L    K+ +L+
Sbjct: 1   VIVVTGKGGVGKTTLAANLAAALAKRGKRVLLI 33


>gnl|CDD|31385 COG1192, Soj, ATPases involved in chromosome partitioning [Cell
           division and chromosome partitioning].
          Length = 259

 Score = 34.4 bits (78), Expect = 0.071
 Identities = 31/180 (17%), Positives = 57/180 (31%), Gaps = 42/180 (23%)

Query: 110 GSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDT---------- 159
           G GKTTT   +A  L     KK+L+  LD           +LG +  ++           
Sbjct: 13  GVGKTTTAVNLAAALAKRGGKKVLLIDLDPQGSL----TSWLGLRPDLEGDLYNLLSGLK 68

Query: 160 --------------LEVIPE-------------QSPEKIAIRATQSARDGGYDAVILDTA 192
                         L++IP                 +++ ++         YD +I+DT 
Sbjct: 69  ERPDILDYTVVIEGLDLIPSNIDLAEGAEIELNAVAKELLLKRLLDPVKDDYDYIIIDTP 128

Query: 193 -GRNHINDSLMQEISEIKSLTNPHEILLVADALTGQDAVHLARNFDKIVDLTGIILTRMD 251
                +  + +     +     P  + L            L +     + + GI++TR D
Sbjct: 129 PSLGVLTLNALAAADHVLIPVQPEFLDLEGLEQLLNTLEDLLKLRRNKLIVVGILITRFD 188


>gnl|CDD|110585 pfam01591, 6PF2K, 6-phosphofructo-2-kinase.  This enzyme occurs as
           a bifunctional enzyme with fructose-2,6-bisphosphatase.
           The bifunctional enzyme catalyses both the synthesis and
           degradation of fructose-2,6-bisphosphate, a potent
           regulator of glycolysis. This enzyme contains a P-loop
           motif.
          Length = 223

 Score = 33.8 bits (78), Expect = 0.10
 Identities = 11/29 (37%), Positives = 17/29 (58%)

Query: 99  SPLVIMLVGLQGSGKTTTTAKIAYHLKTL 127
           S  +I++VGL   GKT  + K+  +L  L
Sbjct: 12  SKTMIVMVGLPARGKTYISKKLTRYLNWL 40


>gnl|CDD|133254 cd00878, Arf_Arl, Arf (ADP-ribosylation factor)/Arl (Arf-like)
           small GTPases.  Arf proteins are activators of
           phospholipase D isoforms.  Unlike Ras proteins they lack
           cysteine residues at their C-termini and therefore are
           unlikely to be prenylated.  Arfs are N-terminally
           myristoylated.  Members of the Arf family are regulators
           of vesicle formation in intracellular traffic that
           interact reversibly with membranes of the secretory and
           endocytic compartments in a GTP-dependent manner.  They
           depart from other small GTP-binding proteins by a unique
           structural device, interswitch toggle, that implements
           front-back communication from N-terminus to the
           nucleotide binding site.  Arf-like (Arl) proteins are
           close relatives of the Arf, but only Arl1 has been shown
           to function in membrane traffic like the Arf proteins.
           Arl2 has an unrelated function in the folding of native
           tubulin, and Arl4 may function in the nucleus.  Most
           other Arf family proteins are so far relatively poorly
           characterized.  Thus, despite their significant sequence
           homologies, Arf family proteins may regulate unrelated
           functions.
          Length = 158

 Score = 33.3 bits (77), Expect = 0.13
 Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 15/61 (24%)

Query: 103 IMLVGLQGSGKTT------------TTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRY 150
           I+++GL G+GKTT            T   I ++++T++ K +     DV     Q+++R 
Sbjct: 2   ILILGLDGAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKNVSFTVWDV---GGQDKIRP 58

Query: 151 L 151
           L
Sbjct: 59  L 59


>gnl|CDD|29986 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
           the NTP binding domain of F1 and V1 H+ATPases, DnaB and
           related helicases as well as bacterial RecA and related
           eukaryotic and archaeal recombinases. This group also
           includes bacterial conjugation proteins and related DNA
           transfer proteins involved in type II and type IV
           secretion..
          Length = 165

 Score = 32.4 bits (73), Expect = 0.26
 Identities = 27/133 (20%), Positives = 56/133 (42%), Gaps = 14/133 (10%)

Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDTLE 161
           +I++ G  GSGKTT   ++A ++ T K  K++   ++       E+L     +  +D L 
Sbjct: 1   LILVFGPTGSGKTTLALQLALNIAT-KGGKVVYVDIEEEIEELTERLIGESLKGALDNLI 59

Query: 162 VI----PEQSPEKIAIRATQSARDGGYDAVILDTAGRNHINDS---------LMQEISEI 208
           ++     + +  ++  +A +    GG D +ILD   R               L +E+ E+
Sbjct: 60  IVFATADDPAAARLLSKAERLRERGGDDLIILDELTRLVRALREIREGYPGELDEELREL 119

Query: 209 KSLTNPHEILLVA 221
                   + ++ 
Sbjct: 120 LERARKGGVTVIF 132


>gnl|CDD|32257 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport
           and metabolism].
          Length = 299

 Score = 32.2 bits (73), Expect = 0.35
 Identities = 26/95 (27%), Positives = 45/95 (47%), Gaps = 9/95 (9%)

Query: 36  RTFLEADVSLEVVQSFSKRVQEKAKGEKILRSIQPGQMVIKIVHDELVEVLGKESIELDL 95
           R+   A V  ++  S +  +QE+ K E I R +   +  I+ V+ +L+E    E  +  L
Sbjct: 22  RSLTAAGVDPDLAYSIAIEIQEELKKEGI-RLVTKDE--IREVYQKLLEKGDPEVAKRYL 78

Query: 96  ------NAPSPLVIMLVGLQGSGKTTTTAKIAYHL 124
                     PL+I++ G  G GK+T   ++A  L
Sbjct: 79  LWRRIRKMKRPLIILIGGASGVGKSTIAGELARRL 113


>gnl|CDD|144508 pfam00931, NB-ARC, NB-ARC domain. 
          Length = 285

 Score = 31.5 bits (72), Expect = 0.46
 Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 4/41 (9%)

Query: 80  DELVEVLGKESIELDLNAPSPLVIMLVGLQGSGKTTTTAKI 120
           D +  ++ K    L   + +  V+ +VG+ G GKTT   +I
Sbjct: 3   DMIEALIEK----LLEMSENLGVVGIVGMGGVGKTTLAKQI 39


>gnl|CDD|36745 KOG1532, KOG1532, KOG1532, GTPase XAB1, interacts with DNA repair
           protein XPA [Replication, recombination and repair].
          Length = 366

 Score = 31.5 bits (71), Expect = 0.52
 Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 4/48 (8%)

Query: 99  SPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQE 146
            P++I++VG+ GSGKTT   ++  HL   KK    + +LD   PA + 
Sbjct: 18  RPVIILVVGMAGSGKTTFMQRLNSHLHA-KKTPPYVINLD---PAVRN 61


>gnl|CDD|31114 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell
           envelope biogenesis, outer membrane].
          Length = 448

 Score = 31.4 bits (71), Expect = 0.57
 Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 5/69 (7%)

Query: 67  SIQPGQMVIKIVHDELVEVLGKESIELDLNAPSPLVIMLVGLQGS-GKTTTTAKIAYHLK 125
            I P   +++      +E++G   +   L+  +P+V     + G+ GKTTTT+ IA+ LK
Sbjct: 78  GIPPTHPLVEAAKAAGIEIIGDIELFYRLSGEAPIV----AITGTNGKTTTTSLIAHLLK 133

Query: 126 TLKKKKILM 134
                 +L 
Sbjct: 134 AAGLDALLG 142


>gnl|CDD|73302 cd02042, ParA, ParA and ParB of Caulobacter crescentus belong to a
           conserved family of bacterial proteins implicated in
           chromosome segregation. ParB binds to DNA sequences
           adjacent to the origin of replication and localizes to
           opposite cell poles shortly following the initiation of
           DNA replication. ParB regulates the ParA ATPase activity
           by promoting nucleotide exchange in a fashion
           reminiscent of the exchange factors of eukaryotic G
           proteins. ADP-bound ParA binds single-stranded DNA,
           whereas the ATP-bound form dissociates ParB from its DNA
           binding sites. Increasing the fraction of ParA-ADP in
           the cell inhibits cell division, suggesting that this
           simple nucleotide switch may regulate cytokinesis. ParA
           shares sequence similarity to a conserved and widespread
           family of ATPases which includes the repA protein of the
           repABC operon in R. etli Sym plasmid. This operon is
           involved in the plasmid replication and partition..
          Length = 104

 Score = 31.0 bits (70), Expect = 0.69
 Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 1/29 (3%)

Query: 110 GSGKTTTTAKIAYHLKTLKKKKILMASLD 138
           G GKTTT   +A  L   + K++L+  LD
Sbjct: 10  GVGKTTTAVNLAAAL-ARRGKRVLLIDLD 37


>gnl|CDD|31889 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related
           GTPases of G3E family [Amino acid transport and
           metabolism].
          Length = 323

 Score = 31.1 bits (70), Expect = 0.72
 Identities = 26/114 (22%), Positives = 50/114 (43%), Gaps = 15/114 (13%)

Query: 92  ELDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYL 151
            L     +  VI + G+ G+GK+T    +   L+  +  ++ + ++D   P     +  L
Sbjct: 43  ALYPRTGNAHVIGITGVPGAGKSTLIEALGRELRE-RGHRVAVLAVDPSSPFTGGSI--L 99

Query: 152 GEQIQVDTLEVIPEQSPEKIAIRAT-----QSARD-------GGYDAVILDTAG 193
           G++I++  L V P         R T     ++ R+        GYD +I++T G
Sbjct: 100 GDRIRMQRLAVDPGVFIRSSPSRGTLGGLSRATREAIKLLDAAGYDVIIVETVG 153


>gnl|CDD|147155 pfam04851, ResIII, Type III restriction enzyme, res subunit. 
          Length = 103

 Score = 31.0 bits (71), Expect = 0.74
 Identities = 17/47 (36%), Positives = 22/47 (46%), Gaps = 4/47 (8%)

Query: 103 IMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLR 149
            ++V   GSGKT T AK+   L   KKK + +    V R    EQ  
Sbjct: 21  GLIVMATGSGKTLTAAKLIARLLKGKKKVLFL----VPRKDLLEQAL 63


>gnl|CDD|146036 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
           protein B.  This protein contains a P-loop.
          Length = 122

 Score = 30.8 bits (70), Expect = 0.77
 Identities = 12/38 (31%), Positives = 22/38 (57%)

Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDV 139
           ++++VG + SGKTT   K+  +LK    +  ++  LD 
Sbjct: 2   IVLVVGPKDSGKTTLIRKLLNYLKRRGYRVAVVKHLDH 39


>gnl|CDD|109652 pfam00604, Flu_PB2, Influenza RNA-dependent RNA polymerase subunit
           PB2.  PB2 can bind 5' end cap structure of RNA.
          Length = 759

 Score = 31.0 bits (70), Expect = 0.78
 Identities = 23/69 (33%), Positives = 28/69 (40%), Gaps = 4/69 (5%)

Query: 245 IILTRMDGDGRGG---AALSMRTVTGKPIKAIGTGEKINDLENFFPDRIANRILGMGDVV 301
             L     +   G   A L    V GK     G    IN+L N      AN ++G GDVV
Sbjct: 673 GALPEDPDEETMGVESAVLRGFLVLGKEDPRYGPALTINELSNLAKGEKANVLIGQGDVV 732

Query: 302 SLVEKAARN 310
            LV K  R+
Sbjct: 733 -LVMKRKRD 740


>gnl|CDD|31829 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
           and repair].
          Length = 845

 Score = 30.7 bits (69), Expect = 0.85
 Identities = 30/112 (26%), Positives = 44/112 (39%), Gaps = 16/112 (14%)

Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILM------ASLDVHRPAAQEQLRYLGEQI 155
           V+++VG  GSGKTT   +           KI        A+  V    A+E    LGE +
Sbjct: 67  VVIIVGETGSGKTTQLPQFLLEEGLGIAGKIGCTQPRRLAARSVAERVAEELGEKLGETV 126

Query: 156 --------QVDTLEVIPEQSPEKIAIRATQSARD-GGYDAVILDTAGRNHIN 198
                   +V     I +   + I +R  Q+     GY  VI+D A    +N
Sbjct: 127 GYSIRFESKVSPRTRI-KVMTDGILLREIQNDPLLSGYSVVIIDEAHERSLN 177


>gnl|CDD|173942 cd08183, Fe-ADH2, Iron-containing alcohol dehydrogenases-like.
           Iron-containing alcohol dehydrogenases (Fe-ADH). Alcohol
           dehydrogenase catalyzes the reduction of acetaldehyde to
           alcohol with NADP as cofactor. Its activity requires
           iron ions. The protein structure represents a
           dehydroquinate synthase-like fold and is a member of the
           iron-activated alcohol dehydrogenase-like family. They
           are distinct from other alcohol dehydrogenases which
           contains different protein domain. Proteins of this
           family have not been characterized. Their specific
           function is unknown. They are mainly found in bacteria.
          Length = 374

 Score = 30.6 bits (70), Expect = 1.0
 Identities = 18/54 (33%), Positives = 23/54 (42%), Gaps = 10/54 (18%)

Query: 146 EQLRYLGEQIQVDTLEVIPEQSPEKIAIRATQSARDGGYDAVI-------LDTA 192
           E LR  G  I+V  + V  E S E +   A   AR+ G D VI       +D  
Sbjct: 41  EALRAAG--IEVTHVVVAGEPSVELVD-AAVAEARNAGCDVVIAIGGGSVIDAG 91


>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
          Length = 489

 Score = 30.4 bits (69), Expect = 1.1
 Identities = 12/25 (48%), Positives = 18/25 (72%)

Query: 98  PSPLVIMLVGLQGSGKTTTTAKIAY 122
           P+P  ++LVG+QG+GK+ T   IA 
Sbjct: 257 PTPRGLLLVGIQGTGKSLTAKAIAN 281


>gnl|CDD|37264 KOG2053, KOG2053, KOG2053, Mitochondrial inheritance and actin
           cytoskeleton organization protein [Cytoskeleton].
          Length = 932

 Score = 30.3 bits (68), Expect = 1.1
 Identities = 16/83 (19%), Positives = 27/83 (32%), Gaps = 1/83 (1%)

Query: 120 IAYHLKTLKKKKILMASLD-VHRPAAQEQLRYLGEQIQVDTLEVIPEQSPEKIAIRATQS 178
                KTL  K I   +L  +    A+   R        +      + S ++       +
Sbjct: 492 AYELYKTLDIKNIQTDTLGHLIFRRAETSGRSSFASNTFNEHLKFYDSSLKETPEYIALA 551

Query: 179 ARDGGYDAVILDTAGRNHINDSL 201
            R G Y  +    A R+ +  SL
Sbjct: 552 YRRGAYSKIPEMLAFRDRLMHSL 574


>gnl|CDD|30909 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
           transport and metabolism].
          Length = 178

 Score = 30.2 bits (68), Expect = 1.3
 Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 8/64 (12%)

Query: 103 IMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQ--VDTL 160
           I+++G  G+GK+T   K+A      KK  +          AA  +   LGE+I+  +D  
Sbjct: 3   ILILGPPGAGKSTLAKKLA------KKLGLPHLDTGDILRAAIAERTELGEEIKKYIDKG 56

Query: 161 EVIP 164
           E++P
Sbjct: 57  ELVP 60


>gnl|CDD|37013 KOG1802, KOG1802, KOG1802, RNA helicase nonsense mRNA reducing
           factor (pNORF1) [RNA processing and modification].
          Length = 935

 Score = 30.0 bits (67), Expect = 1.4
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 3/49 (6%)

Query: 88  KESIELDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMAS 136
             +++  L  P   + ++ G  G+GKT T+A I YHL       +L+ +
Sbjct: 416 SNAVKHVLQRP---LSLIQGPPGTGKTVTSATIVYHLARQHAGPVLVCA 461


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

 Score = 30.1 bits (67), Expect = 1.4
 Identities = 22/100 (22%), Positives = 36/100 (36%), Gaps = 9/100 (9%)

Query: 31  LREIRRTFLEADVSLEVVQSFSKRVQEKAKGEKILRSIQPGQMVIKIVHDELVEVLGKES 90
           LRE+RR        + V +   +   +K    + +        +  I   E  +   KE+
Sbjct: 198 LRELRRAIDLVGEYIGVTEDDFEEALKKVLPSRGVLFEDEDVTLDDIGGLEEAKEELKEA 257

Query: 91  IELDL---------NAPSPLVIMLVGLQGSGKTTTTAKIA 121
           IE  L             P  ++L G  G+GKT     +A
Sbjct: 258 IETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVA 297


>gnl|CDD|73299 cd02036, MinD, Bacterial cell division requires the formation of a
           septum at mid-cell. The site is determined by the min
           operon products MinC, MinD and MinE. MinC is a
           nonspecific inhibitor of the septum protein FtsZ. MinE
           is the supressor of MinC. MinD plays a pivotal role,
           selecting the mid-cell over other sites through the
           activation and regulation of MinC and MinE. MinD is a
           membrane-associated ATPase, related to nitrogenase iron
           protein. More distantly related proteins include
           flagellar biosynthesis proteins and ParA chromosome
           partitioning proteins. MinD is a monomer..
          Length = 179

 Score = 29.8 bits (67), Expect = 1.5
 Identities = 25/111 (22%), Positives = 45/111 (40%), Gaps = 20/111 (18%)

Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKIL------MASLDVHRPAAQEQLRYLGEQI 155
           +++  G  G GKTTTTA +   L  L  K +L      + +LD+           L  ++
Sbjct: 2   IVVTSGKGGVGKTTTTANLGTALAQLGYKVVLIDADLGLRNLDLI--------LGLENRV 53

Query: 156 QVDTLEVIPEQ-----SPEKIAIRATQSARDGGYDAVILDTAGRNHINDSL 201
                +V+        SP  I  R   +A     +A+++ T   + + D+ 
Sbjct: 54  VYTLHDVLAGDYILIDSPAGIE-RGFITAIAPADEALLVTTPEISSLRDAD 103


>gnl|CDD|36142 KOG0924, KOG0924, KOG0924, mRNA splicing factor ATP-dependent RNA
           helicase [RNA processing and modification].
          Length = 1042

 Score = 30.0 bits (67), Expect = 1.6
 Identities = 44/215 (20%), Positives = 77/215 (35%), Gaps = 36/215 (16%)

Query: 3   DNLQERLGSIFQNITGKGSLSETDISNTLREIRRTFLEADVSLEVVQSFSKRVQEKAKGE 62
               +  G+   N+ G        +     E  +      V        S+ V E A  +
Sbjct: 295 KKHWKLAGTALGNVMG--------LEKKNDEDGKVAYRGSVKFASHMKKSEAVSEFASKK 346

Query: 63  KILRSIQPGQMVIKIVHDELVEVLGKESIELDLNAPSPLVIMLVGLQGSGKTTTTAKIAY 122
            I    Q   + +    D+L+ V+ +             V+++VG  GSGKTT  A+  Y
Sbjct: 347 SIRE--QRQYLPVFACRDQLLSVIRENQ-----------VVVIVGETGSGKTTQLAQYLY 393

Query: 123 HLKTLKKKKI------LMASLDVHRPAAQEQLRYLGEQI-------QVDTLEVIPEQSPE 169
                    I       +A++ V +  A+E    LG+ +        V + +   +   +
Sbjct: 394 EDGYADNGMIGCTQPRRVAAISVAKRVAEEMGVTLGDTVGYSIRFEDVTSEDTKIKYMTD 453

Query: 170 KIAIRATQSARD-GGYDAVILDTAGRNHIN-DSLM 202
            I +R +   RD   Y  +I+D A    +N D L 
Sbjct: 454 GILLRESLKDRDLDKYSVIIMDEAHERSLNTDILF 488


>gnl|CDD|29614 cd01567, NAPRTase_PncB, Nicotinate phosphoribosyltransferase
           (NAPRTase) family. Nicotinate phosphoribosyltransferase
           catalyses the formation of NAMN and PPi from
           5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic
           acid, this is the first, and also rate limiting,
           reaction in the NAD salvage synthesis. This salvage
           pathway serves to recycle NAD degradation products..
          Length = 343

 Score = 29.9 bits (67), Expect = 1.6
 Identities = 32/148 (21%), Positives = 47/148 (31%), Gaps = 30/148 (20%)

Query: 212 TNPHEILLVADALTGQDAVHLARNFDKIVDLTGIILTRMDGDGRGGAALSMRTVTGKPIK 271
           T  H  +    AL        AR   +     GI L        G               
Sbjct: 203 TMAHSWIQAFGALEEAAFEAFARWLPQFGGGLGIALIDTYDTDNG--------------- 247

Query: 272 AIGTGEKINDLENFFPDRIANRILGM----GDVVSLVEKAARNLNEKQAALTAKKI-AKG 326
                  +N L+          +LG+    GD V L++K  ++L+E    L  KKI   G
Sbjct: 248 ------FLNALKLAKALGAGGGLLGVRLDSGDPVELIKKVRKHLDELGIDLNKKKIIISG 301

Query: 327 KFDLEDLAEQFRQTQKIG----GIGSIL 350
             D E+  E   +         G+G+ L
Sbjct: 302 DLDTEEAIELLLEQGASPNDAFGVGTSL 329


>gnl|CDD|48380 cd03116, MobB, Molybdenum is an essential trace element in the form
           of molybdenum cofactor (Moco) which is associated with
           the metabolism of nitrogen, carbon and sulfur by redox
           active enzymes. In E. coli, the synthesis of Moco
           involves genes from several loci: moa, mob, mod, moe and
           mog. The mob locus contains mobA and mobB genes. MobB
           catalyzes the attachment of the guanine dinucleotide to
           molybdopterin..
          Length = 159

 Score = 29.8 bits (67), Expect = 1.8
 Identities = 12/26 (46%), Positives = 13/26 (50%)

Query: 100 PLVIMLVGLQGSGKTTTTAKIAYHLK 125
             VI  VG  GSGKTT   K+   L 
Sbjct: 1   MKVIGFVGYSGSGKTTLLEKLIPALS 26


>gnl|CDD|73297 cd02034, CooC, The accessory protein CooC, which contains a
           nucleotide-binding domain (P-loop) near the N-terminus,
           participates in the maturation of the nickel center of
           carbon monoxide dehydrogenase (CODH). CODH from
           Rhodospirillum rubrum catalyzes the reversible oxidation
           of CO to CO2. CODH contains a nickel-iron-sulfur cluster
           (C-center) and an iron-sulfur cluster (B-center). CO
           oxidation occurs at the C-center. Three accessory
           proteins encoded by cooCTJ genes are involved in nickel
           incorporation into a nickel site. CooC functions as a
           nickel insertase that mobilizes nickel to apoCODH using
           energy released from ATP hydrolysis. CooC is a homodimer
           and has NTPase activities. Mutation at the P-loop
           abolishs its function..
          Length = 116

 Score = 29.4 bits (66), Expect = 2.0
 Identities = 27/113 (23%), Positives = 41/113 (36%), Gaps = 13/113 (11%)

Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLD--------VHRPAAQEQLRYLGE 153
            I + G  G GKTT  A +A +L   K K +L    D               + L  +G 
Sbjct: 1   KIAITGKGGVGKTTIAALLARYLAE-KGKPVLAIDADPDDLPERLSVEVGEIKLLLVMGM 59

Query: 154 QIQVDTLEVIPEQSPEKIAIRATQSARDGGYDAVILDT-AGRNHINDSLMQEI 205
                     PE +     +R     RD   + V++DT AG  H+     + +
Sbjct: 60  GRPGGEGCYCPENALLNALLRHLVLTRD---EQVVVDTEAGLEHLGRGTAEGV 109


>gnl|CDD|145019 pfam01656, CbiA, CobQ/CobB/MinD/ParA nucleotide binding domain.
           This family consists of various cobyrinic acid
           a,c-diamide synthases. These include CbiA and CbiP from
           S.typhimurium, and CobQ from R. capsulatus. These
           amidases catalyse amidations to various side chains of
           hydrogenobyrinic acid or cobyrinic acid a,c-diamide in
           the biosynthesis of cobalamin (vitamin B12) from
           uroporphyrinogen III. Vitamin B12 is an important
           cofactor and an essential nutrient for many plants and
           animals and is primarily produced by bacteria. The
           family also contains dethiobiotin synthetases as well as
           the plasmid partitioning proteins of the MinD/ParA
           family.
          Length = 212

 Score = 29.3 bits (66), Expect = 2.1
 Identities = 34/182 (18%), Positives = 60/182 (32%), Gaps = 47/182 (25%)

Query: 110 GSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAA---------QEQLRYLGEQIQ---- 156
           G GKTT  A +A  L   +  ++L+  LD                + L+   E +     
Sbjct: 9   GVGKTTLAANLARALA-KRGYRVLLIDLDPQANLTSSLGKGPDLIDVLKEGLEIVDAQPL 67

Query: 157 ------------VDTLEVIPE----QSPEKIAIRATQSAR--DGGYDAVILDTAGRNHIN 198
                       +D L +IP      + E   I            YD VI+D A      
Sbjct: 68  QHIAAAIVPSRNLDPLLLIPSNLSLANFESELILEGGEEGLIKLAYDYVIIDGAP----- 122

Query: 199 DSLMQEISEIKSLTNPHEILLVADALTGQDAVHLARNFDKIV-----DLTGIILTRMDGD 253
             L +      +L     +++  +      AV  A+   ++V      + G++L ++D  
Sbjct: 123 -GLGELT--ANALVAADILVVPIEP--EGVAVLGAQRLLELVERLGLKILGVVLNKVDRG 177

Query: 254 GR 255
             
Sbjct: 178 DE 179


>gnl|CDD|32636 COG2805, PilT, Tfp pilus assembly protein, pilus retraction ATPase
           PilT [Cell motility and secretion / Intracellular
           trafficking and secretion].
          Length = 353

 Score = 29.4 bits (66), Expect = 2.1
 Identities = 26/109 (23%), Positives = 48/109 (44%), Gaps = 9/109 (8%)

Query: 27  ISNTLREIRRTFLEADVSLEVVQSFSKRVQEKAKGEKILRSIQPGQMVIKIVHDEL--VE 84
           +++  R+I     E D S  +      RV          +      +V++++  ++  +E
Sbjct: 57  LNDDQRKILEENGELDFSYTLPGVARFRVN-------AFKQRGGYALVLRLIPSKIPTLE 109

Query: 85  VLGKESIELDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKIL 133
            LG   I  +L      +I++ G  GSGK+TT A +  ++   K K IL
Sbjct: 110 ELGLPPIVRELAESPRGLILVTGPTGSGKSTTLAAMIDYINKHKAKHIL 158


>gnl|CDD|31532 COG1341, COG1341, Predicted GTPase or GTP-binding protein [General
           function prediction only].
          Length = 398

 Score = 29.5 bits (66), Expect = 2.2
 Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 1/62 (1%)

Query: 81  ELVEVLGKESIELDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVH 140
           E +E +         +A    V+M+VG   SGK+T T  +A  L   + +K+ +   DV 
Sbjct: 54  EPLEEIADTWESKSESAGKVGVVMVVGPVDSGKSTLTTYLANKL-LARGRKVAIIDADVG 112

Query: 141 RP 142
           + 
Sbjct: 113 QS 114


>gnl|CDD|133359 cd04159, Arl10_like, Arl10-like subfamily.  Arl9/Arl10 was
           identified from a human cancer-derived EST dataset.  No
           functional information about the subfamily is available
           at the current time, but crystal structures of human
           Arl10b and Arl10c have been solved.
          Length = 159

 Score = 29.2 bits (66), Expect = 2.2
 Identities = 13/19 (68%), Positives = 13/19 (68%)

Query: 103 IMLVGLQGSGKTTTTAKIA 121
           I LVGLQ SGKTT    IA
Sbjct: 2   ITLVGLQNSGKTTLVNVIA 20


>gnl|CDD|31969 COG1783, XtmB, Phage terminase large subunit [General function
           prediction only].
          Length = 414

 Score = 29.2 bits (65), Expect = 2.3
 Identities = 25/112 (22%), Positives = 42/112 (37%), Gaps = 6/112 (5%)

Query: 103 IMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASL----DVHRPAAQEQLRYLGEQIQVD 158
            +  G +GS K+  TA      K L +  I +  +    + H+ +     +    ++ V 
Sbjct: 27  FIAKGGRGSSKSYATALKNI-EKLLSEPGIDVLVIREVENTHKQSTYALFKEALSELGVT 85

Query: 159 TLEVIPEQSPEKIA-IRATQSARDGGYDAVILDTAGRNHINDSLMQEISEIK 209
               I + SPE I      +    G  D   L +   N I+D   +E SE  
Sbjct: 86  KFFKISKSSPEIILKDTGQRIIFKGLDDPAKLKSIAVNWISDLWFEEASEFS 137


>gnl|CDD|72973 cd03214, ABC_Iron-Siderophores_B12_Hemin, ABC transporters,
           involved in the uptake of siderophores, heme, and
           vitamin B12, are widely conserved in bacteria and
           archaea.  Only very few species lack representatives of
           the siderophore family transporters.  The E. coli BtuCD
           protein is an ABC transporter mediating vitamin B12
           uptake.  The two ATP-binding cassettes (BtuD) are in
           close contact with each other, as are the two
           membrane-spanning subunits (BtuC); this arrangement is
           distinct from that observed for the E. coli lipid
           flippase MsbA.  The BtuC subunits provide 20
           transmembrane helices grouped around a translocation
           pathway that is closed to the cytoplasm by a gate
           region, whereas the dimer arrangement of the BtuD
           subunits resembles the ATP-bound form of the Rad50 DNA
           repair enzyme.  A prominent cytoplasmic loop of BtuC
           forms the contact region with the ATP-binding cassette
           and represent a conserved motif among the ABC
           transporters..
          Length = 180

 Score = 29.2 bits (66), Expect = 2.3
 Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 93  LDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLG 152
           L L+  +  ++ ++G  G+GK+T    +A  LK     +IL+   D+   + +E  R + 
Sbjct: 18  LSLSIEAGEIVGILGPNGAGKSTLLKTLAGLLK-PSSGEILLDGKDLASLSPKELARKIA 76


>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 = 29.2 bits (65), Expect = 2.3
 Identities = 31/196 (15%), Positives = 53/196 (27%), Gaps = 57/196 (29%)

Query: 102 VIMLVGLQGSGKTTTTAKIAYH-----------LKTLKKKKILMASLDVHRPAAQEQLRY 150
           V  LV   G+GK++    +A             LK  +  +++  S +  R     +L  
Sbjct: 3   VSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLSAEDPREEIHRRLEA 62

Query: 151 LGEQIQVDTLEV------------------IPEQSPEKIAIRATQSARDGGYDAVILDTA 192
           + + ++ D                           PE   I           D V++D  
Sbjct: 63  ILQHLEPDDAGDRLFIDSGRIQPISIAREGRIIVVPEFERIIE--QLLIRRIDLVVIDPL 120

Query: 193 GRNHINDSLMQEISEIKSLTNPHEILLVADALTGQDAVHLARNFDKIVDLT--------G 244
              H             S  +   +  V  AL       +A      + L          
Sbjct: 121 VSFH-----------GVSENDNGAMDAVIKALR-----RIAAQTGAAILLVHHVRKGSAK 164

Query: 245 IILTRMDGDGRGGAAL 260
              T+     RG +AL
Sbjct: 165 DGDTQ--EAARGASAL 178


>gnl|CDD|173952 cd08193, HVD, 5-hydroxyvalerate dehydrogenase (HVD) catalyzes the
           oxidation of 5-hydroxyvalerate to 5-oxovalerate with
           NAD+ as cofactor.  5-hydroxyvalerate dehydrogenase (HVD)
           is an iron-containing (type III) NAD-dependent alcohol
           dehydrogenase. It plays a role in the cyclopentanol
           metabolism biochemical pathway. It catalyzes the
           oxidation of 5-hydroxyvalerate to 5-oxovalerate with
           NAD+ as cofactor. This cyclopentanol (cpn) degradation
           pathway is present in some bacteria which can use
           cyclopentanol as sole carbon source. In Comamonas sp.
           strain NCIMB 9872, this enzyme is encoded by the CpnD
           gene.
          Length = 376

 Score = 29.0 bits (66), Expect = 2.4
 Identities = 21/88 (23%), Positives = 35/88 (39%), Gaps = 16/88 (18%)

Query: 118 AKIAYHLKTLKKKKIL------MASLDVHRPAAQEQLRYLGEQIQVDTLEVIPEQSPEKI 171
           A++   L  L  K++L      +    +  P     L   G ++ V   +V  +  PE +
Sbjct: 15  ARLGELLAALGAKRVLVVTDPGILKAGLIDPLLAS-LEAAGIEVTVFD-DVEAD-PPEAV 71

Query: 172 AIRATQSARDGGYDAVI-------LDTA 192
              A ++AR  G D VI       +D A
Sbjct: 72  VEAAVEAARAAGADGVIGFGGGSSMDVA 99


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

 Score = 29.1 bits (65), Expect = 2.4
 Identities = 13/41 (31%), Positives = 24/41 (58%), Gaps = 3/41 (7%)

Query: 98  PSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLD 138
              ++I + G  GSGKTT   +++   + L  +K+++ SLD
Sbjct: 6   EKVIIIGIAGGSGSGKTTVAKELS---EQLGVEKVVVISLD 43


>gnl|CDD|37016 KOG1805, KOG1805, KOG1805, DNA replication helicase [Replication,
           recombination and repair].
          Length = 1100

 Score = 29.2 bits (65), Expect = 2.5
 Identities = 12/33 (36%), Positives = 21/33 (63%), Gaps = 1/33 (3%)

Query: 104 MLVGLQGSGKTTTTAKIAYHLKTLKKKKILMAS 136
           +++G+ G+GKTTT + +   L     KK+L+ S
Sbjct: 689 LILGMPGTGKTTTISLLIKIL-VALGKKVLLTS 720


>gnl|CDD|110578 pfam01583, APS_kinase, Adenylylsulphate kinase.  Enzyme that
           catalyses the phosphorylation of adenylylsulphate to
           3'-phosphoadenylylsulfate. This domain contains an ATP
           binding P-loop motif.
          Length = 157

 Score = 29.2 bits (66), Expect = 2.5
 Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 5/40 (12%)

Query: 100 PLVIMLVGLQGSGKTTTTAKIAYHL-KTLKKKKILMASLD 138
              +   GL GSGK+T    IA  L + L  + I +  LD
Sbjct: 2   GCTVWFTGLSGSGKST----IANALERKLFAQGISVYVLD 37


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

 Score = 29.1 bits (65), Expect = 2.6
 Identities = 12/37 (32%), Positives = 18/37 (48%)

Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLD 138
           +I+L    G GKTT   + A  L T    ++   SL+
Sbjct: 32  LIILTAGTGVGKTTFLREYALDLITQHGVRVGTISLE 68


>gnl|CDD|33900 COG4148, ModC, ABC-type molybdate transport system, ATPase
           component [Inorganic ion transport and metabolism].
          Length = 352

 Score = 29.1 bits (65), Expect = 2.9
 Identities = 12/36 (33%), Positives = 19/36 (52%)

Query: 86  LGKESIELDLNAPSPLVIMLVGLQGSGKTTTTAKIA 121
           LG  +++ +   P+  +  L G  GSGKT+    IA
Sbjct: 10  LGNFALDANFTLPARGITALFGPSGSGKTSLINMIA 45


>gnl|CDD|30190 cd01672, TMPK, Thymidine monophosphate kinase (TMPK), also known as
           thymidylate kinase, catalyzes the phosphorylation of
           thymidine monophosphate (TMP) to thymidine diphosphate
           (TDP) utilizing ATP as its preferred phophoryl donor.
           TMPK represents the rate-limiting step in either de novo
           or salvage biosynthesis of thymidine triphosphate
           (TTP)..
          Length = 200

 Score = 28.7 bits (64), Expect = 3.0
 Identities = 10/33 (30%), Positives = 18/33 (54%)

Query: 101 LVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKIL 133
           + I+  G+ G+GKTT    +A  L+    + +L
Sbjct: 1   MFIVFEGIDGAGKTTLIELLAERLEARGYEVVL 33


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

 Score = 28.7 bits (64), Expect = 3.1
 Identities = 21/88 (23%), Positives = 33/88 (37%), Gaps = 9/88 (10%)

Query: 45  LEVVQSF-SKRVQEKAKGEKILRSIQ---PGQMVIKIVHDELVEVLGKESIELDLNAPSP 100
           L  V+S  SK V E        R      P Q    +  + ++E L    +E D      
Sbjct: 125 LREVESLGSKGVFEVVGESLDPREKVETRPIQSESDVGLETMLEKLWNRLMEDD-----V 179

Query: 101 LVIMLVGLQGSGKTTTTAKIAYHLKTLK 128
            ++ + G+ G GKTT   +I      + 
Sbjct: 180 GIVGIYGMGGVGKTTLARQIFNKFDEVG 207


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

 Score = 28.9 bits (64), Expect = 3.3
 Identities = 24/89 (26%), Positives = 34/89 (38%), Gaps = 10/89 (11%)

Query: 54  RVQEKAKGEKILRSIQPGQMVIKIVHDELVEVLGKESIELDLNAPSPL-------VIMLV 106
              E    + +  +++        VH  L EV  K  + L L     L       V ML 
Sbjct: 284 ARAELRILDSLFVALKIRA---GTVHRLLGEVPAKVKLRLSLEQKEALDVLVVDEVSMLT 340

Query: 107 GLQGSGKTTTTAKIAYHLKTLKKKKILMA 135
           G  G+GKTT    IA  +K     ++L A
Sbjct: 341 GGPGTGKTTAIKAIARLIKEGDGDQLLAA 369


>gnl|CDD|133337 cd04137, RheB, Rheb (Ras Homolog Enriched in Brain) subfamily.
           Rheb was initially identified in rat brain, where its
           expression is elevated by seizures or by long-term
           potentiation.  It is expressed ubiquitously, with
           elevated levels in muscle and brain.  Rheb functions as
           an important mediator between the tuberous sclerosis
           complex proteins, TSC1 and TSC2, and the mammalian
           target of rapamycin (TOR) kinase to stimulate cell
           growth.  TOR kinase regulates cell growth by controlling
           nutrient availability, growth factors, and the energy
           status of the cell.  TSC1 and TSC2 form a dimeric
           complex that has tumor suppressor activity, and TSC2 is
           a GTPase activating protein (GAP) for Rheb.  The
           TSC1/TSC2 complex inhibits the activation of TOR kinase
           through Rheb.  Rheb has also been shown to induce the
           formation of large cytoplasmic vacuoles in a process
           that is dependent on the GTPase cycle of Rheb, but
           independent of the TOR kinase, suggesting Rheb plays a
           role in endocytic trafficking that leads to cell growth
           and cell-cycle progression.  Most Ras proteins contain a
           lipid modification site at the C-terminus, with a
           typical sequence motif CaaX, where a = an aliphatic
           amino acid and X = any amino acid.  Lipid binding is
           essential for membrane attachment, a key feature of most
           Ras proteins.
          Length = 180

 Score = 28.7 bits (65), Expect = 3.4
 Identities = 13/34 (38%), Positives = 24/34 (70%), Gaps = 10/34 (29%)

Query: 74  VIKIVHDELVEVLGKESIELDLNAPSPLVIMLVG 107
           V+K+++D+++++LGKES+      P    I+LVG
Sbjct: 90  VVKVIYDKILDMLGKESV------P----IVLVG 113


>gnl|CDD|29997 cd01131, PilT, Pilus retraction ATPase PilT. PilT is a nucleotide
           binding protein responsible for the retraction of type
           IV pili, likely by pili disassembly. This retraction
           provides the force required for travel of bacteria in
           low water environments by a mechanism known as twitching
           motility..
          Length = 198

 Score = 28.7 bits (64), Expect = 3.6
 Identities = 11/32 (34%), Positives = 19/32 (59%)

Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKIL 133
           ++++ G  GSGK+TT A +  ++   K   IL
Sbjct: 3   LVLVTGPTGSGKSTTLAAMIDYINKNKTHHIL 34


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

 Score = 28.8 bits (64), Expect = 3.6
 Identities = 10/37 (27%), Positives = 15/37 (40%)

Query: 95  LNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKK 131
           L    P  I++ G  G+GKT T   +   L+      
Sbjct: 37  LRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANV 73


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

 Score = 28.3 bits (63), Expect = 4.0
 Identities = 10/26 (38%), Positives = 15/26 (57%)

Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTL 127
           V+ + G  GSGKTT   K++  L+  
Sbjct: 1   VVGIAGPSGSGKTTFAKKLSNQLRVN 26


>gnl|CDD|30835 COG0489, Mrp, ATPases involved in chromosome partitioning [Cell
           division and chromosome partitioning].
          Length = 265

 Score = 28.5 bits (63), Expect = 4.1
 Identities = 39/192 (20%), Positives = 65/192 (33%), Gaps = 44/192 (22%)

Query: 102 VIMLV-GLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLR----------- 149
           VI +  G  G GK+T    +A  L     K++L+   D+  P+    L            
Sbjct: 59  VIAVTSGKGGVGKSTVAVNLAAAL-AQLGKRVLLLDADLRGPSIPRMLGLENLPGLTELL 117

Query: 150 ---YLGEQIQVDTLEVI--------PEQSPEKIAIRATQ----SARDGGYDAVILDTAGR 194
               L   IQ D ++V+        P      +  +A          G YD VI+DT   
Sbjct: 118 AGEALEPVIQHDGIKVLSILPLGPVPVIPRGLLGSKAMLQLLEDVLWGEYDYVIIDTPPG 177

Query: 195 NHIND-SLMQEISEIKSLTNPHEILLVA--DALTGQDAVHLARNFDKI-VDLTGIILTRM 250
               D +++Q I        P  +++V        +D        +K  + + G++    
Sbjct: 178 TGDADATVLQRI--------PDGVVIVTTPGKTALEDVKKAIDMLEKAGIPVLGVVENMS 229

Query: 251 DG----DGRGGA 258
                  G GG 
Sbjct: 230 YFICPRCGEGGG 241


>gnl|CDD|31564 COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General
           function prediction only].
          Length = 398

 Score = 28.5 bits (63), Expect = 4.6
 Identities = 30/133 (22%), Positives = 54/133 (40%), Gaps = 14/133 (10%)

Query: 92  ELDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDV--HRPAAQEQLR 149
            +      P +I+++G +  GKTT    +   +K L ++ I +   D+   R    + LR
Sbjct: 29  LIKKLDLRPFIILILGPRQVGKTTL---LKLLIKGLLEEIIYINFDDLRLDRIELLDLLR 85

Query: 150 YLGEQIQVDTLEVIPE--QSPEKIAIRATQSARDGGYDAVILDTAGRNHINDSLMQEISE 207
              E  + +   +  +  Q+      RA +   D G   V++   G +    S   EISE
Sbjct: 86  AYIELKEREKSYIFLDEIQNVPDW-ERALKYLYDRGNLDVLI--TGSSSSLLSK--EISE 140

Query: 208 IKSLTNPHEILLV 220
             SL    + L +
Sbjct: 141 --SLAGRGKDLEL 151


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

 Score = 28.4 bits (63), Expect = 4.7
 Identities = 32/193 (16%), Positives = 62/193 (32%), Gaps = 27/193 (13%)

Query: 98  PSPLVIM-------LVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRY 150
            SPL  M       ++G   SGKTT   +         ++ +L+      R  +   + +
Sbjct: 18  NSPLCPMTRGTIHVILGPMFSGKTTELLRRIRREIIAGRRVLLIKYAKDTRYESSSIVTH 77

Query: 151 LGEQIQVDTLEVIPEQSPEKIAIRATQSARDGGYDAVILDTAGRNHINDSLMQEISEIKS 210
            G ++    L      S         + A +G  D + +D A                + 
Sbjct: 78  DGIEMPCWALPDASFLS------EFGKDALNGDVDVIGIDEA------QFFGDLYEFCRE 125

Query: 211 LTNPHEILLVADALTGQDAVHLARNFDKIVDLTGIILTRMDGDGR-----GGAALSMRTV 265
           + + H   ++   L G       + F  I+DL  +  +              A  ++R  
Sbjct: 126 VADVHGKTVIVAGLDGD---FKRKPFGAILDLVPLADSVTKLTAVCEECGADARFTLRKT 182

Query: 266 TGKPIKAIGTGEK 278
             K ++ IG  + 
Sbjct: 183 NDKEVEVIGGADV 195


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

 Score = 28.2 bits (63), Expect = 4.9
 Identities = 10/23 (43%), Positives = 15/23 (65%)

Query: 103 IMLVGLQGSGKTTTTAKIAYHLK 125
           I+L+G+ G+GKTT    +A  L 
Sbjct: 2   IVLIGMMGAGKTTVGRLLAKALG 24


>gnl|CDD|35828 KOG0608, KOG0608, KOG0608, Warts/lats-like serine threonine kinases
           [Cell cycle control, cell division, chromosome
           partitioning].
          Length = 1034

 Score = 28.2 bits (62), Expect = 4.9
 Identities = 30/123 (24%), Positives = 58/123 (47%), Gaps = 15/123 (12%)

Query: 36  RTFLEADVSLEVVQSFSKRVQEKAKGEKILRSIQPGQMVIKIVHDELVEVLG-KES--IE 92
           + F+E  V   V++S+ +R + K + EK +           I+ +++ ++L  KES  I 
Sbjct: 566 KFFMEQHVE-NVLKSYQQREKRKKQLEKEMVKAGLPD----IMQNQMRKMLQQKESNYIR 620

Query: 93  L---DLNAPSPLVIMLVGLQGSGKTTTTAKI----AYHLKTLKKKKILMASLDVHRPAAQ 145
           L    ++    + I  +G+   G+     K+     Y +KTL+K  +LM +   H  A +
Sbjct: 621 LKRAKMDKSMFVKIKTIGVGAFGEVCLVRKVDTRALYAMKTLRKADVLMRNQVAHVKAER 680

Query: 146 EQL 148
           + L
Sbjct: 681 DIL 683


>gnl|CDD|38801 KOG3595, KOG3595, KOG3595, Dyneins, heavy chain [Cytoskeleton].
          Length = 1395

 Score = 28.0 bits (62), Expect = 5.4
 Identities = 25/125 (20%), Positives = 47/125 (37%), Gaps = 14/125 (11%)

Query: 1   MFDNLQERLGSIFQNITGKGSLSETDISNTLREIRRTFLEADVSLEVVQSFSKRVQEKAK 60
               LQE L  +F+  + +  L   D  +   +I    L        V+     ++   K
Sbjct: 380 FDKKLQEVLLKLFEADSLQMPLLYGDFRSESHKIYEEVLS-------VELLRGVLEAYLK 432

Query: 61  GEKILRSIQPGQMVIKIVHDELVEVLGKESIELDLNAPSPLVIMLVGLQGSGKTTTTAKI 120
              I       + +  ++  + +E + +  I+  L  P     +LVG+ GSGK + T   
Sbjct: 433 QFNIEE----IRPMHLVLFRDAIEHVLR--IDRILRQPRGHA-LLVGVGGSGKQSLTRLA 485

Query: 121 AYHLK 125
           A+   
Sbjct: 486 AFING 490


>gnl|CDD|39108 KOG3905, KOG3905, KOG3905, Dynein light intermediate chain [Cell
           motility].
          Length = 473

 Score = 28.1 bits (62), Expect = 5.5
 Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 2/67 (2%)

Query: 84  EVLGKESIELDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKIL-MASLDVHRP 142
           E+L + S       PS   ++++G  GSGKT+  +K+    +T+KK   L    L VH  
Sbjct: 36  EILSEVSTRTRSKLPSGKNVLVLGDNGSGKTSLISKLQ-GSETVKKGSGLEYLYLHVHDE 94

Query: 143 AAQEQLR 149
              +  R
Sbjct: 95  DRDDLTR 101


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

 Score = 28.1 bits (62), Expect = 5.5
 Identities = 14/90 (15%), Positives = 30/90 (33%), Gaps = 4/90 (4%)

Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLG---EQIQVD 158
           V+++ G  G+GKT    +  Y     + + +L  S +       E  R  G   E     
Sbjct: 25  VVLITGPPGTGKTIFALQFLYEGAR-EGEPVLYVSTEESPEELLENARSFGWDLEVYIEK 83

Query: 159 TLEVIPEQSPEKIAIRATQSARDGGYDAVI 188
               I +    +  + +         + ++
Sbjct: 84  GKLAILDAFLSEKGLVSIVVGDPLDLEELL 113


>gnl|CDD|33657 COG3867, COG3867, Arabinogalactan endo-1,4-beta-galactosidase
           [Carbohydrate transport and metabolism].
          Length = 403

 Score = 28.1 bits (62), Expect = 5.5
 Identities = 15/54 (27%), Positives = 20/54 (37%), Gaps = 2/54 (3%)

Query: 231 HLARNFDK--IVDLTGIILTRMDGDGRGGAALSMRTVTGKPIKAIGTGEKINDL 282
            +A  + K  +V  T    T  DGDG      S     G PI   G    + D+
Sbjct: 269 DIASRYHKDVMVVETAYTYTLEDGDGHENTFPSSEQTGGYPITVQGQATFVRDV 322


>gnl|CDD|35277 KOG0054, KOG0054, KOG0054, Multidrug resistance-associated
           protein/mitoxantrone resistance protein, ABC superfamily
           [Secondary metabolites biosynthesis, transport and
           catabolism].
          Length = 1381

 Score = 27.9 bits (62), Expect = 6.2
 Identities = 18/85 (21%), Positives = 34/85 (40%), Gaps = 8/85 (9%)

Query: 36  RTFLEADVSLEVVQSFSKRVQEKAKGEKILRSIQPGQMVIKIVHDELVEVLGKESIE--- 92
              ++A VSL+ ++ F    +E           + G+  I+I           ES E   
Sbjct: 481 SQLVQAKVSLKRLKEF-LLSEELDPDSVERSPDEAGENAIEI--KNGSFSWDSESPEPTL 537

Query: 93  --LDLNAPSPLVIMLVGLQGSGKTT 115
             ++       ++ +VG  GSGK++
Sbjct: 538 KDINFEIKKGQLVAVVGPVGSGKSS 562


>gnl|CDD|99868 cd06115, AthCS_per_like, Arabidopsis thaliana (Ath) peroxisomal
           (Per) CS_like. CS catalyzes the condensation of acetyl
           coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate
           and coenzyme A (CoA), the first step in the citric acid
           cycle (TCA or Krebs cycle). The overall CS reaction is
           thought to proceed through three partial reactions and
           involves both closed and open conformational forms of
           the enzyme: a) the carbanion or equivalent is generated
           from AcCoA by base abstraction of a proton, b) the
           nucleophilic attack of this carbanion on OAA to generate
           citryl-CoA, and c) the hydrolysis of citryl-CoA to
           produce citrate and CoA. This group contains three
           Arabidopsis peroxisomal CS proteins, CYS1, -2, and -3
           which are involved in the glyoxylate cycle. AthCYS1, in
           addition to a peroxisomal targeting sequence, has a
           predicted secretory signal peptide; it may be targeted
           to both the secretory pathway and the peroxisomes and is
           thought to be located in the extracellular matrix.
           AthCSY1 is expressed only in siliques and specifically
           in developing seeds. AthCSY2 and 3 are active during
           seed germination and seedling development and are
           thought to participate in the beta-oxidation of fatty
           acids..
          Length = 410

 Score = 27.8 bits (62), Expect = 6.2
 Identities = 13/56 (23%), Positives = 31/56 (55%), Gaps = 5/56 (8%)

Query: 39  LEADVSLEVVQSFSKRVQEKAK-----GEKILRSIQPGQMVIKIVHDELVEVLGKE 89
           L    ++E + +F + V+ + +     G ++ ++  P   +IK + DE+ E++GK+
Sbjct: 265 LAEIGTVENIPAFIEGVKNRKRKLSGFGHRVYKNYDPRAKIIKKLADEVFEIVGKD 320


>gnl|CDD|30200 cd02027, APSK, Adenosine 5'-phosphosulfate kinase (APSK) catalyzes
           the phosphorylation of adenosine 5'-phosphosulfate to
           form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The
           end-product PAPS is a biologically "activated" sulfate
           form important for the assimilation of inorganic
           sulfate..
          Length = 149

 Score = 27.7 bits (62), Expect = 6.6
 Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 5/38 (13%)

Query: 102 VIMLVGLQGSGKTTTTAKIAYHL-KTLKKKKILMASLD 138
           VI L GL GSGK+T    IA  L + L ++   +  LD
Sbjct: 1   VIWLTGLSGSGKST----IARALEEKLFQRGRPVYVLD 34


>gnl|CDD|31393 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
           and repair / Transcription].
          Length = 677

 Score = 27.9 bits (62), Expect = 6.7
 Identities = 15/45 (33%), Positives = 19/45 (42%)

Query: 91  IELDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMA 135
           I  DL +P P+  +L G  GSGKT               +  LMA
Sbjct: 274 ILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEAGYQAALMA 318


>gnl|CDD|31343 COG1149, COG1149, MinD superfamily P-loop ATPase containing an
           inserted ferredoxin domain [Energy production and
           conversion].
          Length = 284

 Score = 27.6 bits (61), Expect = 6.9
 Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 2/41 (4%)

Query: 102 VIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRP 142
           V +  G  G+GKTT  A +A  L    K K+++A  DV  P
Sbjct: 4   VAVASGKGGTGKTTVAANLAVLLG--DKYKLVLADCDVEAP 42


>gnl|CDD|38564 KOG3354, KOG3354, KOG3354, Gluconate kinase [Carbohydrate transport
           and metabolism].
          Length = 191

 Score = 27.7 bits (61), Expect = 7.5
 Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 5/54 (9%)

Query: 96  NAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLR 149
             P   VI+++G+ GSGK+T    ++  L      K +    D+H PA  E++ 
Sbjct: 8   MGPFKYVIVVMGVSGSGKSTIGKALSEEL----GLKFIDGD-DLHPPANVEKMT 56


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

 Score = 27.5 bits (61), Expect = 7.6
 Identities = 13/24 (54%), Positives = 17/24 (70%)

Query: 101 LVIMLVGLQGSGKTTTTAKIAYHL 124
           +VI + GL GSGKTT   ++A HL
Sbjct: 1   MVITISGLPGSGKTTVARELAEHL 24


>gnl|CDD|30597 COG0248, GppA, Exopolyphosphatase [Nucleotide transport and
           metabolism / Inorganic ion transport and metabolism].
          Length = 492

 Score = 27.6 bits (61), Expect = 7.6
 Identities = 23/121 (19%), Positives = 46/121 (38%), Gaps = 14/121 (11%)

Query: 320 AKKIAKGKFDLEDLAEQFRQTQKIGGIGS------ILRMLPGMPSLKQNIMP-SSFDDKT 372
           A+   + +  LE++A+++R     G +G+      + ++     S    ++       + 
Sbjct: 182 ARDAVREE--LEEIAKEYRIAGWAGLVGTSGTIRALAKLHMAQGSYPLRVLHGYEITAEE 239

Query: 373 INHHIAIIASMTKEERANPSIIKHSRKKRIAAGSGTNAAKINKLLKLHRQVAEMMHSTQG 432
           +   +  +  MT EER     +   R   I AG+    A    L      +  M+ S  G
Sbjct: 240 LEKLLERLIRMTSEERLKLEGLSKDRADVILAGAAILEAVFEAL-----SIERMIVSDGG 294

Query: 433 L 433
           L
Sbjct: 295 L 295


>gnl|CDD|72983 cd03224, ABC_TM1139_LivF_branched, LivF (TM1139) is part of the
           LIV-I bacterial ABC-type two-component transport system
           that imports neutral, branched-chain amino acids.  The
           E. coli branched-chain amino acid transporter comprises
           a heterodimer of ABC transporters (LivF and LivG), a
           heterodimer of six-helix TM domains (LivM and LivH), and
           one of two alternative soluble periplasmic substrate
           binding proteins (LivK or LivJ).  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..
          Length = 222

 Score = 27.7 bits (62), Expect = 7.7
 Identities = 15/57 (26%), Positives = 23/57 (40%), Gaps = 1/57 (1%)

Query: 93  LDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLR 149
           + L  P   ++ L+G  G+GKTT    I   L   +   I     D+      E+ R
Sbjct: 19  VSLTVPEGEIVALLGRNGAGKTTLLKTIMGLLPP-RSGSIRFDGRDITGLPPHERAR 74


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

 Score = 27.5 bits (61), Expect = 7.8
 Identities = 12/33 (36%), Positives = 15/33 (45%)

Query: 98  PSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKK 130
           P P  ++L G  G+GKTT    IA  L      
Sbjct: 17  PPPKNLLLYGPPGTGKTTLARAIANELFRPGAP 49


>gnl|CDD|35293 KOG0070, KOG0070, KOG0070, GTP-binding ADP-ribosylation factor Arf1
           [Intracellular trafficking, secretion, and vesicular
           transport].
          Length = 181

 Score = 27.5 bits (61), Expect = 8.0
 Identities = 12/24 (50%), Positives = 15/24 (62%), Gaps = 4/24 (16%)

Query: 103 IMLVGLQGSGKTTTTAKIAYHLKT 126
           I++VGL  +GKTT    I Y LK 
Sbjct: 20  ILMVGLDAAGKTT----ILYKLKL 39


>gnl|CDD|144246 pfam00580, UvrD-helicase, UvrD/REP helicase.  The Rep family
           helicases are composed of four structural domains. The
           Rep family function as dimers. REP helicases catalyse
           ATP dependent unwinding of double stranded DNA to single
           stranded DNA. Bacillus subtilis addA and Escherichia
           coli exodeoxyribonuclease V beta have large insertions
           near to the carboxy-terminus relative to other members
           of the family.
          Length = 494

 Score = 27.7 bits (62), Expect = 8.0
 Identities = 8/18 (44%), Positives = 11/18 (61%), Gaps = 1/18 (5%)

Query: 110 GSGKTTT-TAKIAYHLKT 126
           G+GKT   T +IAY +  
Sbjct: 23  GTGKTRVLTERIAYLILE 40


>gnl|CDD|33915 COG4175, ProV, ABC-type proline/glycine betaine transport system,
           ATPase component [Amino acid transport and metabolism].
          Length = 386

 Score = 27.6 bits (61), Expect = 8.1
 Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 2/31 (6%)

Query: 85  VLGKESIELDLNAPSPLVIMLVGLQGSGKTT 115
           V+G     LD+      VIM  GL GSGK+T
Sbjct: 41  VVGVNDASLDVEEGEIFVIM--GLSGSGKST 69


>gnl|CDD|145224 pfam01935, DUF87, Domain of unknown function DUF87.  The function
           of this prokaryotic domain is unknown. It contains
           several conserved aspartates and histidines that could
           be metal ligands.
          Length = 218

 Score = 27.3 bits (61), Expect = 8.2
 Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 2/31 (6%)

Query: 110 GSGKTTTTAKIAYHLKTLKKKKILMASLDVH 140
           GSGK+ T A +   L   K   +L+   D H
Sbjct: 33  GSGKSNTVAVLLEELLEKKGATVLI--FDPH 61


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

 Score = 27.5 bits (61), Expect = 8.3
 Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 1/65 (1%)

Query: 92  ELDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYL 151
            L+L       ++L+G  GSGKTTT  K+   L      +I +   D+      E  R +
Sbjct: 19  NLNLEIAKGEFLVLIGPSGSGKTTTM-KMINRLIEPTSGEIFIDGEDIREQDPVELRRKI 77

Query: 152 GEQIQ 156
           G  IQ
Sbjct: 78  GYVIQ 82


>gnl|CDD|31396 COG1203, COG1203, Predicted helicases [General function prediction
           only].
          Length = 733

 Score = 27.4 bits (60), Expect = 8.4
 Identities = 25/130 (19%), Positives = 44/130 (33%), Gaps = 8/130 (6%)

Query: 6   QERLGSIFQNITGKGSLSETDISNTLREIRRTFLEADVSLEVVQSFSKRVQEKAKGEKIL 65
              L S    +     LS++      R   R   + D+            QE    + +L
Sbjct: 122 LSSLISEKSFLADWEGLSDSLF----RFFFRLLEKMDIKDTR-NFTELAKQEARLLKPLL 176

Query: 66  RSIQPGQMVIKIV--HDELVEVLGKESIELDLNAPSP-LVIMLVGLQGSGKTTTTAKIAY 122
             +     + K     +     L ++++EL L      L+++L    G GKT  +  +A 
Sbjct: 177 LLLSAIARINKFKSFIEHEGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILAL 236

Query: 123 HLKTLKKKKI 132
            L   K K  
Sbjct: 237 ALLDEKIKLK 246


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

 Score = 27.2 bits (60), Expect = 8.7
 Identities = 10/27 (37%), Positives = 15/27 (55%)

Query: 99  SPLVIMLVGLQGSGKTTTTAKIAYHLK 125
              ++ +VG + SGKTT   K+   LK
Sbjct: 1   MMKILGIVGYKNSGKTTLIEKLVRKLK 27


>gnl|CDD|38349 KOG3139, KOG3139, KOG3139, N-acetyltransferase [General function
           prediction only].
          Length = 165

 Score = 27.2 bits (60), Expect = 9.9
 Identities = 16/68 (23%), Positives = 25/68 (36%), Gaps = 13/68 (19%)

Query: 132 ILMASLDVHRPAAQEQLRYLGEQIQVDTLEVIPEQSPEKIAI----RATQSARDGGYDAV 187
            ++  LD HR   +  +  L          V  E   + I      +A  + R  GY  V
Sbjct: 71  AIVCKLDTHRNTLRGYIAMLA---------VDSEYRGQGIGKALVRKAIDAMRSRGYSEV 121

Query: 188 ILDTAGRN 195
           +L+T   N
Sbjct: 122 VLETEVTN 129


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.316    0.134    0.361 

Gapped
Lambda     K      H
   0.267   0.0775    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,132,969
Number of extensions: 270094
Number of successful extensions: 1250
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1222
Number of HSP's successfully gapped: 151
Length of query: 461
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 364
Effective length of database: 4,167,664
Effective search space: 1517029696
Effective search space used: 1517029696
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (26.4 bits)