RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780638|ref|YP_003065051.1| molecular chaperone protein
DnaJ [Candidatus Liberibacter asiaticus str. psy62]
         (384 letters)



>gnl|CDD|30832 COG0484, DnaJ, DnaJ-class molecular chaperone with C-terminal Zn
           finger domain [Posttranslational modification, protein
           turnover, chaperones].
          Length = 371

 Score =  456 bits (1175), Expect = e-129
 Identities = 207/382 (54%), Positives = 266/382 (69%), Gaps = 12/382 (3%)

Query: 1   MKKADFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQNRNDPEAKEKFAQISEAYEVLRDP 60
           M K D+Y++LG+ ++A++ ++K A+R LA KYHPD+N  D EA+EKF +I+EAYEVL DP
Sbjct: 1   MAKRDYYEILGVSKDASEEEIKKAYRKLAKKYHPDRNPGDKEAEEKFKEINEAYEVLSDP 60

Query: 61  QKRALYDQGGHEALEYGAQSQGAGGFGAGMYGNSDFSELFEGIFGGIMGSGRSYKRSSST 120
           +KRA YDQ GH   + G    G GGFG G +G  DF ++FE  FGG  G G   + +   
Sbjct: 61  EKRAAYDQFGHAGFKAG----GFGGFGFGGFG-GDFGDIFEDFFGG--GGGGRRRPNRP- 112

Query: 121 GEAGADLRYNLEISLEEAFSGKTVQIRFPTAVKCSTCSGSGAKPGTNPMDCNICNGSGRV 180
              GADLRYNLEI+LEEA  G   +IR   +V CSTC GSGAKPGT+P  C  CNGSG+V
Sbjct: 113 -RRGADLRYNLEITLEEAVFGVKKEIRVTRSVTCSTCHGSGAKPGTDPKTCPTCNGSGQV 171

Query: 181 YTTAQS-FFSIERACSTCRGSGQIIPHPCSKCHGQGRVSEEKLLSVNVPPGVDDGTRIRL 239
            T  ++ FFS ++ C TC G+G+II  PC KC G+GRV ++K +SVN+P GVDDG RIRL
Sbjct: 172 RTVQRTGFFSFQQTCPTCNGTGKIIKDPCGKCKGKGRVKKKKSISVNIPAGVDDGDRIRL 231

Query: 240 SGEGGAGVYGGAPGDLYIFISVKKHQFFKRDGADLYCTVPISIVTVAMGGTFDVATLDAT 299
           SGEG AG  GG  GDLY+F+ VK H  F+RDG DLYC VPIS    A+GG  +V TLD  
Sbjct: 232 SGEGEAGPNGGPAGDLYVFVHVKPHPIFERDGDDLYCEVPISFTEAALGGEIEVPTLDGR 291

Query: 300 HSRVTIPEGTQTGKQFRLKGKGMPVINSGRKGDLYVQVQVETPQKLNKRQRELLEEFEQI 359
             ++ IP GTQTG+ FRL+GKGMP + SG +GDLYV+V+VETP+ L+  Q+ELLEEF + 
Sbjct: 292 -VKLKIPAGTQTGEVFRLRGKGMPKLRSGGRGDLYVRVKVETPKNLSDEQKELLEEFAKS 350

Query: 360 SSQDNNPQSTGFFARMKDFFDS 381
              +   QS GFF ++K+FF  
Sbjct: 351 LG-EGPEQSPGFFDKLKNFFKG 371


>gnl|CDD|35931 KOG0712, KOG0712, KOG0712, Molecular chaperone (DnaJ superfamily)
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 337

 Score =  225 bits (575), Expect = 1e-59
 Identities = 135/364 (37%), Positives = 192/364 (52%), Gaps = 36/364 (9%)

Query: 1   MKKADFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQNRNDPEAKEKFAQISEAYEVLRDP 60
           +K    Y +LG+  +A++ ++K A+R LA+KYHPD+N   P+A EKF +IS+AYEVL DP
Sbjct: 1   VKNTKLYDILGVSPDASEEEIKKAYRKLALKYHPDKN---PDAGEKFKEISQAYEVLSDP 57

Query: 61  QKRALYDQGGHEALEYGAQSQGAGGFGAGMYGNSDFSELFEGIFGGIMGSGRSYKRSSST 120
           +KR +YDQ G E L         GG G G  G       F   FG     GR  +R    
Sbjct: 58  EKREIYDQYGEEGL-------QGGGGGGGFGG-------FSQFFGFGGNGGRGRQR---- 99

Query: 121 GEAGADLRYNLEISLEEAFSGKTVQIRFPTAVKCSTCSGSGAKPGTNPMDCNICNGSGRV 180
              G D+ + L+++LEE + GK+ ++       CS CSGSG K G+ P  C  C GSG  
Sbjct: 100 ---GKDVVHQLKVTLEELYMGKSKKLFLSRNFICSKCSGSGGKSGSAP-KCTTCRGSGVQ 155

Query: 181 YTTAQS----FFSIERACSTCRGSGQIIP--HPCSKCHGQGRVSEEKLLSVNVPPGVDDG 234
             T Q       S +  C +C GSG+ I     C  C G   V E+K+L V+V PG+  G
Sbjct: 156 TRTRQMGPGMVQSPQLVCDSCNGSGETISLKDRCKTCSGAKVVREKKILEVHVEPGMPHG 215

Query: 235 TRIRLSGEGGAGVYGGAPGDLYIFISVKKHQFFKRDGADLYCTVPISIVTVAMGGTFDVA 294
            +I   GE      G  PGD+ + I  K+H  F R G+DLY  + IS+V    G      
Sbjct: 216 QKITFKGEADE-APGTKPGDVVLLIDQKEHPGFDRRGSDLYRKLTISLVEALCGFQRVWE 274

Query: 295 TLDATHSRVTIPEG--TQTGKQFRLKGKGMPVINSGRKGDLYVQVQVETPQKLNKRQREL 352
           TLD    +++   G     G   R++G+GMP+  +  KGDLY++ +V+ P KL+  Q ++
Sbjct: 275 TLDGRLLKLSSKPGEVISPGDTKRVEGEGMPIFRNP-KGDLYIKFEVKFP-KLSPSQLKM 332

Query: 353 LEEF 356
           LE+ 
Sbjct: 333 LEDL 336


>gnl|CDD|35934 KOG0715, KOG0715, KOG0715, Molecular chaperone (DnaJ superfamily)
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 288

 Score =  186 bits (474), Expect = 8e-48
 Identities = 97/284 (34%), Positives = 134/284 (47%), Gaps = 35/284 (12%)

Query: 1   MKKADFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQNRNDPEAKEKFAQISEAYEVLRDP 60
           + K D+Y+VLG+ RNAT  ++K+AFR LA KYHPD N+ D EA +KF +ISEAYE+L D 
Sbjct: 40  ISKEDYYKVLGVSRNATLSEIKSAFRKLAKKYHPDVNK-DKEASKKFKEISEAYEILSDE 98

Query: 61  QKRALYDQGGHEALEYGAQSQGAGGFGAGMYGNSDFSELFEGIFGGIMGSGRSYKRSSST 120
           +KR  YD  G E                      +  ++F   FGG M      KR    
Sbjct: 99  EKRQEYDVYGLEQHGEFG---------------GNPFDVFLEFFGGKM-----NKRVP-- 136

Query: 121 GEAGADLRYNLEISLEEAFSGKTVQIRFPTAVKCSTCSGSGAKPGTNPMDCNICNGSGRV 180
                D  Y+L +  +EA  G   +I F     C TC GSGA+ G     C  C+G G V
Sbjct: 137 ---DKDQYYDLSLDFKEAVRGSKKRISFNVLSDCETCFGSGAEEGAKRESCKTCSGRGLV 193

Query: 181 YTTAQSFFSIERACSTCRGSGQIIPHPCSKCHGQGRVSEEKLLSVNVPPGVDDGTRIRLS 240
               +  F +   CS C G G ++   C  C G G+V   K + + +P GV     +R +
Sbjct: 194 SNPKEDPFILY-TCSYCLGRGLVLRDNCQACSGAGQVRRAKDIMIVLPAGVRSADTLRFA 252

Query: 241 GEGGAGVYGGAPGDLYIFISVKKHQFFKRDGADLYCTVPISIVT 284
           G G          DL++ + V K   F+R+G D+     IS   
Sbjct: 253 GHGND--------DLFVRLIVAKSPSFRREGKDILYDAIISFTQ 288


>gnl|CDD|35932 KOG0713, KOG0713, KOG0713, Molecular chaperone (DnaJ superfamily)
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 336

 Score =  170 bits (431), Expect = 6e-43
 Identities = 109/349 (31%), Positives = 151/349 (43%), Gaps = 40/349 (11%)

Query: 5   DFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQNRNDPEAKEKFAQISEAYEVLRDPQKRA 64
           DFY++LG+ +NA+D+++K A+R LA+KYHPD+N +DP A EKF +I+ AYEVL DP+KR 
Sbjct: 17  DFYELLGVPKNASDQEIKKAYRKLALKYHPDKNPDDPNANEKFKEINAAYEVLSDPEKRK 76

Query: 65  LYDQGGHEALEYGAQSQGAGGFGAGMYGNSDFSELFEGIFGGIMGSGRSYKRSSSTGEA- 123
            YD  G E L+             G  GN  FS  F      + G+           EA 
Sbjct: 77  HYDTYGEEGLK-----DENKDGEGGGGGNDIFSAFFGDFGVTVGGNPL--------EEAL 123

Query: 124 --GADLRYNLEISLEEAFSGKTVQIRFPTAVKCSTCSGSGAKPGTNPMDCNICNGSGRVY 181
             G+D+  +LE  LE  + G  V+      V                       G  ++ 
Sbjct: 124 PKGSDVSSDLEKQLEHFYMGNFVEEVREKGVYKPAPGTRKCNCRLEMFTQQEGPGRFQML 183

Query: 182 TTAQSFFSIERACSTCRGSGQIIPHPCSKCHGQGRVSEEKLLSVNVPPGVDDGTRIRLSG 241
             A                       C +C     V EE  L V    G  DG       
Sbjct: 184 QEAV----------------------CDECPNVKLVLEEDPLEVEFERGDADGPEEIFEL 221

Query: 242 EGGAGVYGGAPGDLYIFISVKKHQFFKRDGADLYCTVPISIVTVAMGGTFDVATLDATHS 301
           EG   +  G PGDL+  I    H  F+R G DLY  V IS+    +G   ++  LD  + 
Sbjct: 222 EGEPHID-GVPGDLFFKIVSYTHPRFERKGDDLYTNVTISLEAALVGFEMEILHLDGHYV 280

Query: 302 RVTIPEGTQTGKQFRLKGKGMPVI-NSGRKGDLYVQVQVETPQKLNKRQ 349
            V+  + T  G + R KG+GMP++ N   KG+LYV   VE P+      
Sbjct: 281 EVSRKKITWPGARTRKKGEGMPLLKNRNEKGNLYVTFDVEFPKSSLSDS 329


>gnl|CDD|144958 pfam01556, DnaJ_C, DnaJ C terminal region.  This family consists of
           the C terminal region form the DnaJ protein. Although
           the function of this region is unknown, it is always
           found associated with pfam00226 and pfam00684. DnaJ is a
           chaperone associated with the Hsp70 heat-shock system
           involved in protein folding and renaturation after
           stress.
          Length = 101

 Score =  136 bits (344), Expect = 1e-32
 Identities = 53/101 (52%), Positives = 67/101 (66%), Gaps = 1/101 (0%)

Query: 253 GDLYIFISVKKHQFFKRDGADLYCTVPISIVTVAMGGTFDVATLDATHSRVTIPEGTQTG 312
           GDLY+ I VK H  FKRDG DLY T+PIS+    +GGT +V TLD    ++ IP GTQ G
Sbjct: 1   GDLYVVIKVKPHPVFKRDGNDLYVTLPISLKEALLGGTVEVPTLDGRKLKIKIPAGTQPG 60

Query: 313 KQFRLKGKGMPVI-NSGRKGDLYVQVQVETPQKLNKRQREL 352
              R+KGKGMP+   SG +GDL V   V+ P+KL+  Q+EL
Sbjct: 61  DVLRIKGKGMPIFKGSGGRGDLIVTFNVKIPKKLSSEQKEL 101



 Score = 39.4 bits (93), Expect = 0.002
 Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 1/43 (2%)

Query: 221 KLLSVNVPPGVDDGTRIRLSGEG-GAGVYGGAPGDLYIFISVK 262
           + L + +P G   G  +R+ G+G       G  GDL +  +VK
Sbjct: 47  RKLKIKIPAGTQPGDVLRIKGKGMPIFKGSGGRGDLIVTFNVK 89



 Score = 29.8 bits (68), Expect = 1.1
 Identities = 12/24 (50%), Positives = 15/24 (62%)

Query: 124 GADLRYNLEISLEEAFSGKTVQIR 147
           G DL   L ISL+EA  G TV++ 
Sbjct: 19  GNDLYVTLPISLKEALLGGTVEVP 42


>gnl|CDD|143981 pfam00226, DnaJ, DnaJ domain.  DnaJ domains (J-domains) are
          associated with hsp70 heat-shock system and it is
          thought that this domain mediates the interaction.
          DnaJ-domain is therefore part of a chaperone (protein
          folding) system. The T-antigens, although not in
          Prosite are confirmed as DnaJ containing domains from
          literature.
          Length = 63

 Score =  113 bits (286), Expect = 7e-26
 Identities = 39/63 (61%), Positives = 55/63 (87%)

Query: 5  DFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQNRNDPEAKEKFAQISEAYEVLRDPQKRA 64
          D+Y++LG+ R+A+D ++K A+R LA+KYHPD+N  DPEA+EKF +I+EAYEVL DP+KRA
Sbjct: 1  DYYEILGVPRDASDEEIKKAYRKLALKYHPDKNPGDPEAEEKFKEINEAYEVLSDPEKRA 60

Query: 65 LYD 67
          +YD
Sbjct: 61 IYD 63


>gnl|CDD|35933 KOG0714, KOG0714, KOG0714, Molecular chaperone (DnaJ superfamily)
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 306

 Score = 99.0 bits (245), Expect = 2e-21
 Identities = 90/326 (27%), Positives = 138/326 (42%), Gaps = 26/326 (7%)

Query: 3   KADFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQN-RNDPEAKEKFAQISEAYEVLRDPQ 61
             D+Y++LGI R+A++  +K A+R LA+KYHPD+N      A+ KF +I+EAYEVL DP+
Sbjct: 2   GKDYYKILGIARSASEEDIKKAYRKLALKYHPDKNPSPKEVAEAKFKEIAEAYEVLSDPK 61

Query: 62  KRALYDQGGHEALEYGAQSQGAGGFGAGMYGNSDFSELFEGIFGGIMGSGRSYKRSSSTG 121
           KR +YDQ G E L+ G     +       +      + F   FG    S           
Sbjct: 62  KRKIYDQYGEEGLKGGGSFSSSFTSELFYFLFRKPDKDFYEFFG---VSSPFSGSKKGYR 118

Query: 122 EAGADLRYNLEISLEEAFSGKTVQIRFPTAVKCSTCSGSGAKPGTNPMDCNICNGSGRVY 181
           +  A        S  +AF       R       S  S   + P  +P+            
Sbjct: 119 DKNAAPGEEAFKSEGKAFQSLYGPKRKQYDSSGSDRSARQSPPVEHPLRV---------- 168

Query: 182 TTAQSFFSIERACSTCRGSGQIIPHPCSKCHGQGRVSEEKLLSVNVPPGVDDGTRIRLSG 241
                  S+E          +I     +   G+   S  + LS+++ PG  +GT+I    
Sbjct: 169 -------SLEDLYKGESKKMKISRQSFTSN-GREGSSRSRYLSISIKPGWKEGTKITFPE 220

Query: 242 EGGAGVYGGAPGDLYIFISVKKHQFFKRDGADLYCTVP--ISIVTVAMGGTFDVATLDAT 299
           EG     G  P D+   +  K H  F RDG DL  +    IS+    +G T  V TLD  
Sbjct: 221 EGD-EEPGILPADIEFVVDEKPHPLFSRDGNDLSYSSGYEISLKEALLGVTVFVPTLDGR 279

Query: 300 HSRVTIPEGT-QTGKQFRLKGKGMPV 324
              ++I +   + G++  + G+G+P 
Sbjct: 280 SYSLSINKDLIEPGEEDVIPGEGLPC 305


>gnl|CDD|35910 KOG0691, KOG0691, KOG0691, Molecular chaperone (DnaJ superfamily)
          [Posttranslational modification, protein turnover,
          chaperones].
          Length = 296

 Score = 94.0 bits (233), Expect = 6e-20
 Identities = 40/97 (41%), Positives = 56/97 (57%)

Query: 2  KKADFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQNRNDPEAKEKFAQISEAYEVLRDPQ 61
          K  D+Y +LGI  +ATD ++K A+R  A++YHPD+N  DP+A EKF ++SEAYEVL D +
Sbjct: 3  KDTDYYDLLGISEDATDAEIKKAYRKKALQYHPDKNPGDPQAAEKFQELSEAYEVLSDEE 62

Query: 62 KRALYDQGGHEALEYGAQSQGAGGFGAGMYGNSDFSE 98
           RA YD+          +   A GF      +    E
Sbjct: 63 SRAAYDKLRKSGSSAQGREDQADGFRKKFGSDLFERE 99


>gnl|CDD|99751 cd06257, DnaJ, DnaJ domain or J-domain.  DnaJ/Hsp40 (heat shock
          protein 40) proteins are highly conserved and play
          crucial roles in protein translation, folding,
          unfolding, translocation, and degradation. They act
          primarily by stimulating the ATPase activity of Hsp70s,
          an important chaperonine family. Hsp40 proteins are
          characterized by the presence of a J domain, which
          mediates the interaction with Hsp70. They may contain
          other domains as well, and the architectures provide a
          means of classification..
          Length = 55

 Score = 92.6 bits (231), Expect = 2e-19
 Identities = 32/55 (58%), Positives = 46/55 (83%)

Query: 5  DFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQNRNDPEAKEKFAQISEAYEVLRD 59
          D+Y +LG+  +A+D ++K A+R LA+KYHPD+N +DPEA+EKF +I+EAYEVL D
Sbjct: 1  DYYDILGVPPDASDEEIKKAYRKLALKYHPDKNPDDPEAEEKFKEINEAYEVLSD 55


>gnl|CDD|35935 KOG0716, KOG0716, KOG0716, Molecular chaperone (DnaJ superfamily)
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 279

 Score = 89.8 bits (222), Expect = 1e-18
 Identities = 35/70 (50%), Positives = 50/70 (71%)

Query: 5   DFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQNRNDPEAKEKFAQISEAYEVLRDPQKRA 64
           D Y VLG+ + AT  ++K A+R LA+KYHPD+N ++PEA +KF +I+ AY +L DP KR 
Sbjct: 32  DLYDVLGLPKTATKDEIKKAYRKLALKYHPDKNGDNPEATDKFKEINTAYAILSDPTKRN 91

Query: 65  LYDQGGHEAL 74
           +YD+ G   L
Sbjct: 92  VYDEYGELGL 101


>gnl|CDD|144326 pfam00684, DnaJ_CXXCXGXG, DnaJ central domain (4 repeats).  The
           central cysteine-rich (CR) domain of DnaJ proteins
           contains four repeats of the motif CXXCXGXG where X is
           any amino acid. The isolated cysteine rich domain folds
           in zinc dependent fashion. Each set of two repeats binds
           one unit of zinc. Although this domain has been
           implicated in substrate binding, no evidence of specific
           interaction between the isolated DNAJ cysteine rich
           domain and various hydrophobic peptides has been found.
          Length = 79

 Score = 86.7 bits (215), Expect = 1e-17
 Identities = 33/79 (41%), Positives = 39/79 (49%), Gaps = 4/79 (5%)

Query: 141 GKTVQIRFPTAVKCSTCSGSGAKPGTNPMDCNICNGSGRVYT---TAQSFFSIERACSTC 197
           G T  I     V C  C G+GAKPG  P  C  CNGSG V     T    F  ++ C  C
Sbjct: 1   GTTKTITLSRKVTCPHCHGTGAKPGKKPKTCPTCNGSGVVVRVQRTPGGVFQFQQTCPAC 60

Query: 198 RGSGQII-PHPCSKCHGQG 215
            G+G+II   PC  C G+G
Sbjct: 61  GGTGKIIEKDPCKVCKGKG 79


>gnl|CDD|35843 KOG0624, KOG0624, KOG0624, dsRNA-activated protein kinase inhibitor
           P58, contains TPR and DnaJ domains [Defense mechanisms].
          Length = 504

 Score = 84.7 bits (209), Expect = 4e-17
 Identities = 41/116 (35%), Positives = 64/116 (55%), Gaps = 9/116 (7%)

Query: 3   KADFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQNRNDPE---AKEKFAQISEAYEVLRD 59
           K D+Y++LG+ RNA+ +++  A+R LA K+HPD  +++ E   A++KF  I+ A EVL D
Sbjct: 393 KRDYYKILGVKRNASKQEITKAYRKLAQKWHPDNFQDEEEKKKAEKKFIDIAAAKEVLSD 452

Query: 60  PQKRALYDQGGHEALEYGAQSQGAGGFGAGMYGNSDFSELFEGIFGGIMGSGRSYK 115
           P+KR  +D  G + L+  +Q  G GG   G +    F       FGG       + 
Sbjct: 453 PEKRRQFDN-GEDPLDPESQQGGGGGPFHGFWNEHGF-----NPFGGGGPFQFKFH 502


>gnl|CDD|32396 COG2214, CbpA, DnaJ-class molecular chaperone [Posttranslational
           modification, protein turnover, chaperones].
          Length = 237

 Score = 84.5 bits (207), Expect = 5e-17
 Identities = 65/274 (23%), Positives = 103/274 (37%), Gaps = 53/274 (19%)

Query: 5   DFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQNRNDP-EAKEKFAQISEAYEVLRDPQKR 63
           D+Y++LG+  NA+  ++K A+R LA+KYHPD+N  DP  A+EKF +I+EAYE+L DP++R
Sbjct: 7   DYYEILGVPPNASLEEIKKAYRKLALKYHPDRNPGDPKVAEEKFKEINEAYEILSDPERR 66

Query: 64  ALYDQGGHEALEYGAQSQGAGGFGAGMYGNSDFSELFEGIFGGIMGSGRSYKRSSSTGEA 123
           A YD+ G +    G   + +  F   + G+   + L+E   G    +    K S +   +
Sbjct: 67  AEYDKIGADNYFPGKSYRESAAF--PIEGSLQLTGLYEEWRGK--RNKTERKASLADLLS 122

Query: 124 GADLRYNLEISLEEAFSGKTV-QIRFPTAVKCSTCSGSGAKPGTNPMDCNICNGSGRVYT 182
                    +SL    +      +R          +   A  G                 
Sbjct: 123 RGLSGLAAALSLFADEAALRSGSLRRRDLAANLADNFEEALAGVK--------------- 167

Query: 183 TAQSFFSIERACSTCRGSGQIIPHPCSKCHGQGRVSEEKLLSVNVPPGVDDGTRIRLSGE 242
                                                 K L   +  G  +G  +RL G 
Sbjct: 168 ------------------------------KAVARLLGKALKSTIKAGALEGKALRLKGL 197

Query: 243 GGAGVYGGAPGDLYIFISVKKHQFFKRDGADLYC 276
             +    GA G   +    K+H  F  +G D Y 
Sbjct: 198 LKSA--RGALGKARLKELSKRHPPFALEGDDKYP 229


>gnl|CDD|35936 KOG0717, KOG0717, KOG0717, Molecular chaperone (DnaJ superfamily)
          [Posttranslational modification, protein turnover,
          chaperones].
          Length = 508

 Score = 81.3 bits (200), Expect = 5e-16
 Identities = 34/67 (50%), Positives = 48/67 (71%), Gaps = 1/67 (1%)

Query: 2  KKADFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQNR-NDPEAKEKFAQISEAYEVLRDP 60
          KK  +Y+VLG++R+A D ++K  +R LA++YHPD+N     EA ++F  I  AYEVL DP
Sbjct: 6  KKRCYYEVLGVERDADDDEIKKNYRKLALQYHPDKNPDRIEEATQQFQLIQAAYEVLSDP 65

Query: 61 QKRALYD 67
          Q+RA YD
Sbjct: 66 QERAWYD 72


>gnl|CDD|35937 KOG0718, KOG0718, KOG0718, Molecular chaperone (DnaJ superfamily)
          [Posttranslational modification, protein turnover,
          chaperones].
          Length = 546

 Score = 80.0 bits (197), Expect = 1e-15
 Identities = 34/75 (45%), Positives = 52/75 (69%), Gaps = 5/75 (6%)

Query: 5  DFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQNRNDPE----AKEKFAQISEAYEVLRDP 60
          + Y +L + ++ATD ++K A+R L+  +HPD++  DP+    A+EKF +I  AYEVL DP
Sbjct: 10 ELYALLNLPKDATDEEIKKAYRRLSRLFHPDKHT-DPDQKKAAEEKFQRIQRAYEVLSDP 68

Query: 61 QKRALYDQGGHEALE 75
          QKRA+YD  G + L+
Sbjct: 69 QKRAIYDNYGEQGLK 83


>gnl|CDD|35938 KOG0719, KOG0719, KOG0719, Molecular chaperone (DnaJ superfamily)
          [Posttranslational modification, protein turnover,
          chaperones].
          Length = 264

 Score = 75.8 bits (186), Expect = 2e-14
 Identities = 33/70 (47%), Positives = 53/70 (75%), Gaps = 2/70 (2%)

Query: 3  KADFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQN--RNDPEAKEKFAQISEAYEVLRDP 60
          K D Y+VLG++R+ATD++++ A+  LA++ HPD+N   +  EA EKF Q+ +AY++L D 
Sbjct: 13 KKDLYEVLGVERDATDKEIRKAYHKLALRLHPDKNHEEDKVEATEKFQQLQKAYQILSDE 72

Query: 61 QKRALYDQGG 70
          +KRA+YD+ G
Sbjct: 73 EKRAVYDETG 82


>gnl|CDD|35940 KOG0721, KOG0721, KOG0721, Molecular chaperone (DnaJ superfamily)
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 230

 Score = 74.2 bits (182), Expect = 5e-14
 Identities = 36/139 (25%), Positives = 64/139 (46%), Gaps = 19/139 (13%)

Query: 1   MKKADFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQNRNDPEAKEKFAQISEAYEVLRDP 60
            +K D Y++LG+D  A+++++K A+R L++KYHPD+   +   +E F  I++AY+ L D 
Sbjct: 96  RQKFDPYEILGLDPGASEKEIKKAYRRLSIKYHPDKQPPEEGDEEFFEAIAKAYQALTDK 155

Query: 61  QKRALYDQGGHEALEYGAQSQGAGGFGAGM--------YGNSDFSELFEGIFGGI---MG 109
           + R  +++ G+          G      G+           S     F G+  G+   + 
Sbjct: 156 KSRENWEKYGNP--------DGPQATSFGIALPKWIVDKEGSPGVLGFYGLVFGVILPVF 207

Query: 110 SGRSYKRSSSTGEAGADLR 128
            GR + RS      G    
Sbjct: 208 VGRWWYRSRGYTGDGVHFV 226


>gnl|CDD|35941 KOG0722, KOG0722, KOG0722, Molecular chaperone (DnaJ superfamily)
          [Posttranslational modification, protein turnover,
          chaperones].
          Length = 329

 Score = 71.6 bits (175), Expect = 3e-13
 Identities = 29/65 (44%), Positives = 44/65 (67%), Gaps = 1/65 (1%)

Query: 3  KADFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQNRNDPEAKEKFAQISEAYEVLRDPQK 62
            + Y VLG+ R A   ++  A+R LA ++HPD+NR DPE+K+ F +I+ AYE+L+D + 
Sbjct: 32 AENCYDVLGVAREANKSEIAKAYRQLARRHHPDRNR-DPESKKLFVKIATAYEILKDNET 90

Query: 63 RALYD 67
          R  YD
Sbjct: 91 RTQYD 95


>gnl|CDD|35770 KOG0550, KOG0550, KOG0550, Molecular chaperone (DnaJ superfamily)
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 486

 Score = 64.4 bits (156), Expect = 5e-11
 Identities = 37/96 (38%), Positives = 55/96 (57%), Gaps = 10/96 (10%)

Query: 2   KKADFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQNR-NDPEAKEKFAQISEAYEVLRDP 60
           K+ D+Y++LGI RNA+D ++K A+R LA+ +HPD+N  +  EA+ KF ++ EAY +L DP
Sbjct: 371 KRKDWYKILGISRNASDDEIKKAYRKLALVHHPDKNAGSQKEAEAKFKEVGEAYTILSDP 430

Query: 61  QKRALYDQGGHEALEYGAQS-------QGAGGFGAG 89
            KR  +D G  + LE                 F A 
Sbjct: 431 MKRVRFDSG--QDLEEVGSGGAGFDPFNIFRAFQAL 464


>gnl|CDD|34966 COG5407, SEC63, Preprotein translocase subunit Sec63 [Intracellular
           trafficking and secretion].
          Length = 610

 Score = 61.6 bits (149), Expect = 4e-10
 Identities = 26/72 (36%), Positives = 44/72 (61%), Gaps = 5/72 (6%)

Query: 5   DFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQNRNDP-----EAKEKFAQISEAYEVLRD 59
           D Y++LGID++ ++R +K  +R L+MK+HPD+          E +EK+  I++AY +L D
Sbjct: 99  DPYEILGIDQDTSERDIKKRYRMLSMKFHPDKAPPMVNELRSEYEEKYKTITKAYGLLTD 158

Query: 60  PQKRALYDQGGH 71
            ++R  Y   G 
Sbjct: 159 KKRRENYLNYGT 170


>gnl|CDD|35939 KOG0720, KOG0720, KOG0720, Molecular chaperone (DnaJ superfamily)
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 490

 Score = 60.4 bits (146), Expect = 8e-10
 Identities = 26/64 (40%), Positives = 36/64 (56%), Gaps = 1/64 (1%)

Query: 5   DFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQNRNDPEAKEKFAQISEAYEVLRDPQKRA 64
           D Y  LG+  + +D  LK  +R  AM  HPD+N   P A+E F ++  A+EV+ D  KR 
Sbjct: 236 DAYSALGLPSDCSDADLKKNYRKKAMLVHPDKNMI-PRAEEAFKKLQVAFEVIGDSVKRK 294

Query: 65  LYDQ 68
            YD 
Sbjct: 295 EYDL 298


>gnl|CDD|37000 KOG1789, KOG1789, KOG1789, Endocytosis protein RME-8, contains DnaJ
            domain [Intracellular trafficking, secretion, and
            vesicular transport, Posttranslational modification,
            protein turnover, chaperones].
          Length = 2235

 Score = 52.8 bits (126), Expect = 2e-07
 Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 7/61 (11%)

Query: 1    MKKADFYQVLGIDRNATDR----QLKTAFRSLAMKYHPDQNRNDPEAKEKFAQISEAYEV 56
            M      ++L +D    +     +++  +  LA KYHPD+N   PE +E F ++++AYE+
Sbjct: 1278 MSVDLAREILSVDLTNEEHDKPAKIRRQYYKLAAKYHPDKN---PEGREMFERVNKAYEL 1334

Query: 57   L 57
            L
Sbjct: 1335 L 1335


>gnl|CDD|34866 COG5269, ZUO1, Ribosome-associated chaperone zuotin [Translation,
           ribosomal structure and biogenesis / Posttranslational
           modification, protein turnover, chaperones].
          Length = 379

 Score = 50.1 bits (119), Expect = 9e-07
 Identities = 26/74 (35%), Positives = 35/74 (47%), Gaps = 11/74 (14%)

Query: 2   KKADFYQVLGIDR---NATDRQLKTAFRSLAMKYHPDQ-----NRNDPEAKEKFAQISEA 53
           KK D Y +LG+ +    A   Q+  A +    KYHPD+     N+   E    F  I +A
Sbjct: 41  KKVDLYALLGLSKYRTKAIPPQILKAHKKKVYKYHPDKTAAGGNKGCDEF---FKLIQKA 97

Query: 54  YEVLRDPQKRALYD 67
            EVL D + R  YD
Sbjct: 98  REVLGDRKLRLQYD 111


>gnl|CDD|36365 KOG1150, KOG1150, KOG1150, Predicted molecular chaperone (DnaJ
           superfamily) [Posttranslational modification, protein
           turnover, chaperones].
          Length = 250

 Score = 44.7 bits (105), Expect = 4e-05
 Identities = 20/58 (34%), Positives = 36/58 (62%), Gaps = 1/58 (1%)

Query: 7   YQVLGIDRNATDRQLKTAFRSLAMKYHPDQNRND-PEAKEKFAQISEAYEVLRDPQKR 63
           ++VL ID   TD  +K  +R L++  HPD+N +D   A++ F  + +AY++L + + R
Sbjct: 56  FEVLQIDPEVTDEDIKKRYRKLSILVHPDKNPDDAERAQKAFDIVKKAYKLLENDKIR 113


>gnl|CDD|38024 KOG2813, KOG2813, KOG2813, Predicted molecular chaperone, contains
           DnaJ domain [Posttranslational modification, protein
           turnover, chaperones].
          Length = 406

 Score = 43.6 bits (102), Expect = 9e-05
 Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 15/68 (22%)

Query: 150 TAVKCSTCSGSGAKPGTNPMDCNICNGSGRVYTTAQSFFSIERACSTCRGSGQIIPHPCS 209
           T + C +C+G           C +C+G G             + C TC+G G+    PC+
Sbjct: 216 TPMHCMSCTGVPPPKIGTHDLCYMCHGRGI------------KECHTCKGRGKK---PCT 260

Query: 210 KCHGQGRV 217
            C G G +
Sbjct: 261 TCSGTGSL 268


>gnl|CDD|31274 COG1076, DjlA, DnaJ-domain-containing proteins 1
          [Posttranslational modification, protein turnover,
          chaperones].
          Length = 174

 Score = 40.7 bits (95), Expect = 7e-04
 Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 5/52 (9%)

Query: 20 QLKTAFRSLAMKYHPDQNRNDPEAK-----EKFAQISEAYEVLRDPQKRALY 66
           LK  +R L   YHPD+     EA+     ++ A+++ AY+ L+DP  RA Y
Sbjct: 19 ALKLQYRELQRAYHPDRFGKASEAEQRKALQQSAEVNPAYQTLKDPLLRAEY 70



 Score = 39.9 bits (93), Expect = 0.001
 Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 7/61 (11%)

Query: 5   DFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQ--NRNDPE-----AKEKFAQISEAYEVL 57
           D  +VLG++  A    +K A+R L  + HPD+   +          KEK  +I EAYE +
Sbjct: 114 DALKVLGVEIKADQDAIKKAYRKLLSEQHPDKAAAKGLKLEFIEKLKEKLQEIQEAYEDI 173

Query: 58  R 58
           +
Sbjct: 174 K 174


>gnl|CDD|35788 KOG0568, KOG0568, KOG0568, Molecular chaperone (DnaJ superfamily)
          [Posttranslational modification, protein turnover,
          chaperones].
          Length = 342

 Score = 40.2 bits (93), Expect = 9e-04
 Identities = 16/50 (32%), Positives = 30/50 (60%), Gaps = 1/50 (2%)

Query: 5  DFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQNRNDPEAKEKFAQISEAY 54
          + +++LG++  A   +++ AF  LA + HPD    + +A  +F QI EA+
Sbjct: 48 ECFRILGVEEGADADEVREAFHDLAKQVHPDSGSEEADA-ARFIQIDEAF 96


>gnl|CDD|31448 COG1256, FlgK, Flagellar hook-associated protein [Cell motility and
           secretion].
          Length = 552

 Score = 33.1 bits (75), Expect = 0.12
 Identities = 14/67 (20%), Positives = 27/67 (40%)

Query: 318 KGKGMPVINSGRKGDLYVQVQVETPQKLNKRQRELLEEFEQISSQDNNPQSTGFFARMKD 377
            G G+ V++  R  D ++  Q       +        +  Q+ S  + P  +     + D
Sbjct: 56  VGTGVNVVSIQRLRDEFLTNQYRNANSQSSYLDTRASQLSQLESLLSEPSESSLSTLLND 115

Query: 378 FFDSLKN 384
           FF+SL+ 
Sbjct: 116 FFNSLQE 122


>gnl|CDD|35942 KOG0723, KOG0723, KOG0723, Molecular chaperone (DnaJ superfamily)
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 112

 Score = 32.7 bits (74), Expect = 0.20
 Identities = 14/57 (24%), Positives = 30/57 (52%), Gaps = 4/57 (7%)

Query: 1   MKKADFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQNRNDPEAKEKFAQISEAYEVL 57
           M + +   +LG+  +    ++K A R + +  HPD+  +   A    ++I+EA ++L
Sbjct: 53  MSRREAALILGVTPSLDKDKIKEAHRRIMLANHPDRGGSPYLA----SKINEAKDLL 105


>gnl|CDD|153390 cd07321, Extradiol_Dioxygenase_3A_like, Subunit A of Class III
          extradiol dioxygenases.  Extradiol dioxygenases
          catalyze the incorporation of both atoms of molecular
          oxygen into substrates using a variety of reaction
          mechanisms, resulting in the cleavage of aromatic
          rings.  There are two major groups of dioxygenases
          according to the cleavage site of the aromatic ring.
          Intradiol enzymes cleave the aromatic ring between two
          hydroxyl groups, whereas extradiol enzymes cleave the
          aromatic ring between a hydroxylated carbon and an
          adjacent non-hydroxylated carbon. Extradiol
          dioxygenases can be divided into three classes. Class I
          and II enzymes are evolutionary related and show
          sequence similarity, with the two domain class II
          enzymes evolving from the class I enzyme through gene
          duplication. Class III enzymes are different in
          sequence and structure and usually have two subunits,
          designated A and B, which form a tetramer composed of
          two copies of each subunit. This model represents
          subunit A of class III extradiol dioxygenase enzymes.
          The A subunit is the smaller, non-catalytic subunit.
          Enzymes that belong to this family include
          Protocatechuate 4,5-dioxygenase (LigAB) A subunit,
          2'-aminobiphenyl-2,3-diol 1,2-dioxygenase (CarB) A
          subunit, Gallate Dioxygenase and proteins of unknown
          function.
          Length = 77

 Score = 32.3 bits (74), Expect = 0.23
 Identities = 15/63 (23%), Positives = 18/63 (28%), Gaps = 12/63 (19%)

Query: 40 DPEAKEKFAQISEAY-----------EVLRDPQKRALYDQGGHEALEYGAQSQGAGGFGA 88
           PE KE+F    EA              L      ALY  G +  L     +   G   A
Sbjct: 15 KPEVKERFKADPEAVLAEYGLTPEEKAALLARDVGALYVLGVNPMLLMHF-AIRLGIPSA 73

Query: 89 GMY 91
             
Sbjct: 74 EYS 76


>gnl|CDD|146940 pfam04546, Sigma70_ner, Sigma-70, non-essential region.  The
          domain is found in the primary vegetative sigma factor.
          The function of this domain is unclear and can be
          removed without loss of function.
          Length = 210

 Score = 30.6 bits (70), Expect = 0.77
 Identities = 11/21 (52%), Positives = 15/21 (71%), Gaps = 1/21 (4%)

Query: 40 DPE-AKEKFAQISEAYEVLRD 59
          DPE A+E+FA++ E YE  R 
Sbjct: 75 DPEEARERFAELREQYEKTRK 95


>gnl|CDD|31304 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains
           DnaJ-type Zn finger domain [DNA replication,
           recombination, and repair].
          Length = 715

 Score = 30.3 bits (68), Expect = 0.85
 Identities = 20/72 (27%), Positives = 28/72 (38%), Gaps = 15/72 (20%)

Query: 152 VKCSTCSGSGAKPGTNPMDCNICNGSGRVYTTAQSFFSIERACSTCRG------SGQIIP 205
            KC  C G G        +C +C+G+G         F  +   +  R       S +I  
Sbjct: 3   KKCPECGGKGKIVVGEE-ECPVCHGTGFSDD-----FDPKGVANLSRETVDLFASFEI-- 54

Query: 206 HPCSKCHGQGRV 217
            PC KC G+G V
Sbjct: 55  -PCPKCRGKGTV 65


>gnl|CDD|38402 KOG3192, KOG3192, KOG3192, Mitochondrial J-type chaperone
          [Posttranslational modification, protein turnover,
          chaperones].
          Length = 168

 Score = 30.0 bits (67), Expect = 1.1
 Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 6/48 (12%)

Query: 19 RQLKTAFRSLAMKYHPDQNRNDPEAKEKFAQISEAYEVLRDPQKRALY 66
          ++L      L+     DQ      A E+ A++++AY+ L+DP  RA Y
Sbjct: 36 KKLHPDRPGLSFAGDTDQ------ASEQSAELNKAYDTLKDPLARARY 77


>gnl|CDD|48533 cd02984, TRX_PICOT, TRX domain, PICOT (for PKC-interacting cousin
          of TRX) subfamily; PICOT is a protein that interacts
          with protein kinase C (PKC) theta, a calcium
          independent PKC isoform selectively expressed in
          skeletal muscle and T lymphocytes. PICOT contains an
          N-terminal TRX-like domain, which does not contain the
          catalytic CXXC motif, followed by one to three
          glutaredoxin domains. The TRX-like domain is required
          for interaction with PKC theta. PICOT inhibits the
          activation of c-Jun N-terminal kinase and the
          transcription factors, AP-1 and NF-kB, induced by PKC
          theta or T-cell activating stimuli..
          Length = 97

 Score = 29.0 bits (65), Expect = 2.2
 Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 1/37 (2%)

Query: 20 QLKTAFRSLAMKYHPDQNRNDPEAKEKFAQISEAYEV 56
          Q+   F  LA +  P       EA E+  +ISE +E+
Sbjct: 31 QMNQVFEELAKEAFPSVLFLSIEA-EELPEISEKFEI 66


>gnl|CDD|36526 KOG1312, KOG1312, KOG1312, DHHC-type Zn-finger proteins [General
           function prediction only].
          Length = 341

 Score = 28.4 bits (63), Expect = 3.1
 Identities = 14/28 (50%), Positives = 16/28 (57%), Gaps = 3/28 (10%)

Query: 148 FPTAVKCSTCSGSGAKPGTNPMDCNICN 175
           FP  VKCSTC     KP  +   C+ICN
Sbjct: 145 FPKNVKCSTC--KIRKPARSK-HCSICN 169


>gnl|CDD|31264 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General
           function prediction only].
          Length = 339

 Score = 28.2 bits (63), Expect = 3.5
 Identities = 18/72 (25%), Positives = 25/72 (34%), Gaps = 8/72 (11%)

Query: 230 GVDDGTRIRLSGEGGAGVYG-------GAPGDLYIFISVKKHQFFKRDGADLYCTVPISI 282
            V  G  + + G GG G          GA   + I  S +K +  K+ GAD       S 
Sbjct: 163 NVKPGKWVAVVGAGGLGHMAVQYAKAMGAE-VIAITRSEEKLELAKKLGADHVINSSDSD 221

Query: 283 VTVAMGGTFDVA 294
              A+    D  
Sbjct: 222 ALEAVKEIADAI 233


>gnl|CDD|147197 pfam04906, Tweety, Tweety.  The tweety (tty) gene has not been
           characterized at the protein level. However, it is
           thought to form a membrane protein with five potential
           membrane-spanning regions. A number of potential
           functions have been suggested in.
          Length = 406

 Score = 28.1 bits (63), Expect = 3.9
 Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 14/68 (20%)

Query: 85  GFGAGMYGNSDFSELFEGIFGGIMGSGRSYKR---------SSSTGEAGADLRYNLEISL 135
             G G YGNS+ +   +G++  +  S R+            S +T      L  +L   L
Sbjct: 76  AIGVGFYGNSETN---DGVY-QLTYSLRNANHTVSGIDNLVSDTTNSLNETLEQHLT-RL 130

Query: 136 EEAFSGKT 143
           EE F+ +T
Sbjct: 131 EEIFAKRT 138


>gnl|CDD|48580 cd03031, GRX_GRX_like, Glutaredoxin (GRX) family, GRX-like domain
           containing protein subfamily; composed of
           uncharacterized eukaryotic proteins containing a
           GRX-like domain having only one conserved cysteine,
           aligning to the C-terminal cysteine of the CXXC motif of
           GRXs. This subfamily is predominantly composed of plant
           proteins. GRX is a glutathione (GSH) dependent
           reductase, catalyzing the disulfide reduction of target
           proteins via a redox active CXXC motif using a similar
           dithiol mechanism employed by TRXs. GRX has preference
           for mixed GSH disulfide substrates, in which it uses a
           monothiol mechanism where only the N-terminal cysteine
           is required. Proteins containing only the C-terminal
           cysteine are generally redox inactive..
          Length = 147

 Score = 28.3 bits (63), Expect = 3.9
 Identities = 13/48 (27%), Positives = 19/48 (39%), Gaps = 6/48 (12%)

Query: 154 CSTCSGSGAKPGTNPMDCNICNGSGRVYTTAQSFFSIERACSTCRGSG 201
           C  C G+   P      C+ CNGS +V+    +       C  C  +G
Sbjct: 102 CEGCGGARFVP------CSECNGSCKVFAENATAAGGFLRCPECNENG 143


>gnl|CDD|173868 cd08503, PBP2_NikA_DppA_OppA_like_17, The substrate-binding
           component of an uncharacterized ABC-type
           nickel/dipeptide/oligopeptide-like import system
           contains the type 2 periplasmic binding fold.  This CD
           represents the substrate-binding domain of an
           uncharacterized ATP-binding cassette (ABC) type
           nickel/dipeptide/oligopeptide-like transporter. The
           oligopeptide-binding protein OppA and the
           dipeptide-binding protein DppA show significant sequence
           similarity to NikA, the initial nickel receptor. The
           DppA binds dipeptides and some tripeptides and is
           involved in chemotaxis toward dipeptides, whereas the
           OppA binds peptides of a wide range of lengths (2-35
           amino acid residues) and plays a role in recycling of
           cell wall peptides, which precludes any involvement in
           chemotaxis. Most of other periplasmic binding proteins
           are comprised of only two globular subdomains
           corresponding to domains I and III of the
           dipeptide/oligopeptide binding proteins. The structural
           topology of these domains is most similar to that of the
           type 2 periplasmic binding proteins (PBP2), which are
           responsible for the uptake of a variety of substrates
           such as phosphate, sulfate, polysaccharides,
           lysine/arginine/ornithine, and histidine.  The PBP2 bind
           their ligand in the cleft between these domains in a
           manner resembling a Venus flytrap. After binding their
           specific ligand with high affinity, they can interact
           with a cognate membrane transport complex comprised of
           two integral membrane domains and two cytoplasmically
           located ATPase domains. This interaction triggers the
           ligand translocation across the cytoplasmic membrane
           energized by ATP hydrolysis.  Besides transport
           proteins, the PBP2 superfamily includes the
           ligand-binding domains from ionotropic glutamate
           receptors, LysR-type transcriptional regulators,  and
           unorthodox sensor proteins involved in signal
           transduction.
          Length = 460

 Score = 27.5 bits (62), Expect = 7.0
 Identities = 20/83 (24%), Positives = 26/83 (31%), Gaps = 23/83 (27%)

Query: 1   MKKADFYQVLGIDRNATDRQLKTAFRSLAMKYHPDQNR---NDPEAKEKFAQ-ISEAYEV 56
             K  F       R   D+ L  A+RS A       N     +PE         +E    
Sbjct: 368 WMKKPFSATYWGGRPTGDQMLSLAYRSGAP-----WNETHWANPEFDALLDAARAEL--- 419

Query: 57  LRDPQKRA---------LYDQGG 70
             D  KR          L+D+GG
Sbjct: 420 --DEAKRKELYAEMQQILHDEGG 440


>gnl|CDD|32035 COG1850, RbcL, Ribulose 1,5-bisphosphate carboxylase, large subunit
           [Carbohydrate transport and metabolism].
          Length = 429

 Score = 26.8 bits (59), Expect = 9.8
 Identities = 10/36 (27%), Positives = 17/36 (47%)

Query: 246 GVYGGAPGDLYIFISVKKHQFFKRDGADLYCTVPIS 281
            V G   GD   ++   K  FF++D A +    P++
Sbjct: 316 TVVGKLEGDREDYVESDKEFFFEQDWAHIKPVFPVA 351


  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
   0.317    0.135    0.396 

Gapped
Lambda     K      H
   0.267   0.0711    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,629,088
Number of extensions: 246610
Number of successful extensions: 756
Number of sequences better than 10.0: 1
Number of HSP's gapped: 682
Number of HSP's successfully gapped: 51
Length of query: 384
Length of database: 6,263,737
Length adjustment: 96
Effective length of query: 288
Effective length of database: 4,189,273
Effective search space: 1206510624
Effective search space used: 1206510624
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.2 bits)