RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780700|ref|YP_003065113.1| serine protease DO-like
protease [Candidatus Liberibacter asiaticus str. psy62]
         (489 letters)



>gnl|CDD|30614 COG0265, DegQ, Trypsin-like serine proteases, typically
           periplasmic, contain C-terminal PDZ domain
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 347

 Score =  209 bits (532), Expect = 1e-54
 Identities = 112/286 (39%), Positives = 162/286 (56%), Gaps = 5/286 (1%)

Query: 99  PILSDTVERLMFGSGFFITDDGYILTSNHIVEDGASFSVILSDDTELPAKLVGTDALFDL 158
           P           GSGF I+ DGYI+T+NH++      +V L+D  E+PAKLVG D + DL
Sbjct: 62  PSDPPLRSAEGLGSGFIISSDGYIVTNNHVIAGAEEITVTLADGREVPAKLVGKDPISDL 121

Query: 159 AVLKVQSDRKFIPVEFEDANNIRVGEAVFTIGNPFRLRGTVSAGIVSALDRD---IPDRP 215
           AVLK+        +   D++ +RVG+ V  IGNPF L  TV++GIVSAL R         
Sbjct: 122 AVLKIDGAGGLPVIALGDSDKLRVGDVVVAIGNPFGLGQTVTSGIVSALGRTGVGSAGGY 181

Query: 216 GTFTQIDAPINQGNSGGPCFNALGHVIGVNAMIVTSGQFHMGVGLIIPLSIIKKAIPSLI 275
             F Q DA IN GNSGGP  N  G V+G+N  I+       G+G  IP++++   +  LI
Sbjct: 182 VNFIQTDAAINPGNSGGPLVNIDGEVVGINTAIIAPSGGSSGIGFAIPVNLVAPVLDELI 241

Query: 276 SKGRVDHGWFGIMTQNLTQELAIPLGLRGTKGSLITAVVKESPADKAGMKVGDVICMLDG 335
           SKG+V  G+ G++ + LT ++A  LGL    G+++  V+  SPA KAG+K GD+I  ++G
Sbjct: 242 SKGKVVRGYLGVIGEPLTADIA--LGLPVAAGAVVLGVLPGSPAAKAGIKAGDIITAVNG 299

Query: 336 RIIKSHQDFVWQIASRSPKEQVKISLCKEGSKHSVAVVLGSSPTAK 381
           + + S  D V  +AS  P ++V + L + G +  +AV LG      
Sbjct: 300 KPVASLSDLVAAVASNRPGDEVALKLLRGGKERELAVTLGDRSPLS 345


>gnl|CDD|36534 KOG1320, KOG1320, KOG1320, Serine protease [Posttranslational
           modification, protein turnover, chaperones].
          Length = 473

 Score = 92.7 bits (230), Expect = 2e-19
 Identities = 81/326 (24%), Positives = 134/326 (41%), Gaps = 46/326 (14%)

Query: 86  FRKDFHKFFSGEEPILSDTVERLMFGSGFFITDDGYILTSNHIVEDGA-----SFSVILS 140
           F K  + F  G+ P L+        GSGF +  DG I+T+ H+V         S +V+L 
Sbjct: 149 FWKGMNPFELGDIPSLN--------GSGFVVGGDGIIVTNGHVVRVEPRIYAHSSTVLLR 200

Query: 141 DDTEL--------PAKLVGTDALFDLAVLKVQSDRKFIPV-EFEDANNIRVGEAVFTIGN 191
              +            +VG D +  +A LK+++    + V     +++ R G  V  IGN
Sbjct: 201 VQIDAAIGPGNSGEPVIVGVDKVAGVAFLKIKTPENILYVIPLGVSSHFRTGVEVSAIGN 260

Query: 192 PFRLRGTVSAGIVSALDRDIPDRPGTFT-------QIDAPINQGNSGGPCFNALGHVIGV 244
            F L  T++ G+VS   R                 Q DA IN GNSGGP  N  G VIGV
Sbjct: 261 GFGLLNTLTQGMVSGQLRKSFKLGLETGVLISKINQTDAAINPGNSGGPLLNLDGEVIGV 320

Query: 245 NAMIVTSGQFHMGVGLIIPLSIIKKAIPSLISKGRV---------DHGWFGIMTQNLTQE 295
           N   VT   F  G+   IP+  +   +  L                H + G+ +  +   
Sbjct: 321 NTRKVTRIGFSHGISFKIPIDTVLVIVLRLGEFQISLRPVKPLVPVHQYIGLPSYYIFAG 380

Query: 296 LAIPLGLR-------GTKGSLITAVVKESPADKAGMKVGDVICMLDGRIIKSHQDFVWQI 348
           L      +         +  L++ V+  S     G+K GD +  ++G+ +K+ +     I
Sbjct: 381 LVFVPLTKSYIFPSGVVQLVLVSQVLPGSINGGYGLKPGDQVVKVNGKPVKNLKHLYELI 440

Query: 349 ASRSPKEQVKISLCKEGSKHSVAVVL 374
              S +++V + L +  ++ +   +L
Sbjct: 441 EECSTEDKVAV-LDRRSAEDATLEIL 465



 Score = 48.8 bits (116), Expect = 3e-06
 Identities = 81/385 (21%), Positives = 139/385 (36%), Gaps = 39/385 (10%)

Query: 106 ERLMFGSGFFITDDGYILTSNHIVE---DGASFSV-ILSDDTELPAKLVGTDALFDLAVL 161
           +    GSGF I     +LT+ H+V    D    +V       +  A +       DLAV+
Sbjct: 84  QFSSGGSGFAIYG-KKLLTNAHVVAPNNDHKFVTVKKHGSPRKYKAFVAAVFEECDLAVV 142

Query: 162 KVQSDRKFIPVEF-EDANNIRVGEAVFTIGNPFRLRG---TVSAGIVSALDRDIPDRPGT 217
            ++S+      EF +  N   +G+     G+ F + G    V+ G V  ++  I     T
Sbjct: 143 YIESE------EFWKGMNPFELGDIPSLNGSGFVVGGDGIIVTNGHVVRVEPRIYAHSST 196

Query: 218 FT---QIDAPINQGNSGGPCFNALGHVIGVNAMIVTSGQFHMGVGLIIPLSIIKKAIPSL 274
                QIDA I  GNSG P    +  V GV  + + + +    +  +IPL +       +
Sbjct: 197 VLLRVQIDAAIGPGNSGEPVIVGVDKVAGVAFLKIKTPE---NILYVIPLGVSSHFRTGV 253

Query: 275 ISKG-RVDHGWFGIMTQNLTQ-ELAIPLGLRGTKGSLITAVVKESPADKAGMKVGDVICM 332
                    G    +TQ +   +L     L    G LI+ + +   A   G   G  +  
Sbjct: 254 EVSAIGNGFGLLNTLTQGMVSGQLRKSFKLGLETGVLISKINQTDAAINPG-NSGGPLLN 312

Query: 333 LDGRII------KSHQDFVWQIASRSPKEQVKISLCKEGSKHSVAVVLGSSPTAK----N 382
           LDG +I       +   F   I+ + P + V + + + G        +            
Sbjct: 313 LDGEVIGVNTRKVTRIGFSHGISFKIPIDTVLVIVLRLGEFQISLRPVKPLVPVHQYIGL 372

Query: 383 DMHLEVGD--KELLGMVLQDINDGNKKLVRIVALNPNREREVEAKGIQKGMTIVSVNTHE 440
             +          L         G  +LV +  + P         G++ G  +V VN   
Sbjct: 373 PSYYIFAGLVFVPLTKSYIF-PSGVVQLVLVSQVLPGSING--GYGLKPGDQVVKVNGKP 429

Query: 441 VSCIKDVERLIGKAKEKKRDSVLLQ 465
           V  +K +  LI +   + + +VL +
Sbjct: 430 VKNLKHLYELIEECSTEDKVAVLDR 454


>gnl|CDD|29044 cd00987, PDZ_serine_protease, PDZ domain of tryspin-like serine
           proteases, such as DegP/HtrA, which are oligomeric
           proteins involved in heat-shock response, chaperone
           function, and apoptosis. May be responsible for
           substrate recognition and/or binding, as most PDZ
           domains bind C-terminal polypeptides, though binding to
           internal (non-C-terminal) polypeptides and even to
           lipids has been demonstrated. In this subfamily of
           protease-associated PDZ domains a C-terminal beta-strand
           forms the peptide-binding groove base, a circular
           permutation with respect to PDZ domains found in
           Eumetazoan signaling proteins..
          Length = 90

 Score = 72.2 bits (177), Expect = 3e-13
 Identities = 36/90 (40%), Positives = 56/90 (62%)

Query: 283 GWFGIMTQNLTQELAIPLGLRGTKGSLITAVVKESPADKAGMKVGDVICMLDGRIIKSHQ 342
            W G+  Q+LT +LA  LGL+ TKG L+ +V   SPA KAG+K GDVI  ++G+ +KS  
Sbjct: 1   PWLGVTVQDLTPDLAEELGLKDTKGVLVASVDPGSPAAKAGLKPGDVILAVNGKPVKSVA 60

Query: 343 DFVWQIASRSPKEQVKISLCKEGSKHSVAV 372
           D    +A   P ++V +++ + G + +V V
Sbjct: 61  DLRRALAELKPGDKVTLTVLRGGKELTVTV 90



 Score = 32.6 bits (74), Expect = 0.23
 Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 12/83 (14%)

Query: 393 LLGMVLQDIND--------GNKKLVRIVALNPNREREVEAKGIQKGMTIVSVNTHEVSCI 444
            LG+ +QD+           + K V + +++P         G++ G  I++VN   V  +
Sbjct: 2   WLGVTVQDLTPDLAEELGLKDTKGVLVASVDPGSP--AAKAGLKPGDVILAVNGKPVKSV 59

Query: 445 KDVERLIGKAKEKKRDSVLLQIK 467
            D+ R + +   K  D V L + 
Sbjct: 60  ADLRRALAEL--KPGDKVTLTVL 80


>gnl|CDD|143870 pfam00089, Trypsin, Trypsin. 
          Length = 218

 Score = 58.6 bits (142), Expect = 4e-09
 Identities = 37/177 (20%), Positives = 59/177 (33%), Gaps = 33/177 (18%)

Query: 102 SDTVERLMFGSGFFITDDGYILTSNHIVEDGASFSVILSDDT---------------ELP 146
           S  V       G  +  + ++LT+ H V +  S  V+L                    + 
Sbjct: 17  SLQVSSGKHFCGGSLISENWVLTAAHCVSNAKSVRVVLGAHNIVLREGGEQKFDVEKIIV 76

Query: 147 AKLVGTDALFDLAVLKVQSDRKF----IPVEFEDANNIR-VGEAVFTIG----NPFRLRG 197
                 D L D+A+LK++S         P+    A++   VG      G        L  
Sbjct: 77  HPNYNPDTLNDIALLKLKSPVTLGDTVRPICLPTASSDLPVGTTCTVSGWGNTKTLGLPD 136

Query: 198 TVSAGIVSALDRDIPDRPG------TFTQIDAP---INQGNSGGPCFNALGHVIGVN 245
           T+    V  + R+            T     A      QG+SGGP   + G +IG+ 
Sbjct: 137 TLQEVTVPVVSRETCRSAYGGTVTDTMICAGAGGKDACQGDSGGPLVCSDGELIGIV 193


>gnl|CDD|36635 KOG1421, KOG1421, KOG1421, Predicted signaling-associated protein
           (contains a PDZ domain) [General function prediction
           only].
          Length = 955

 Score = 56.2 bits (135), Expect = 2e-08
 Identities = 72/329 (21%), Positives = 131/329 (39%), Gaps = 38/329 (11%)

Query: 101 LSDTVERLMF-GSGFFI-TDDGYILTSNHIVEDG-ASFSVILSDDTELPAKLVGTDALFD 157
             DT        +GF +    GYILT+ H+V  G    S +  +  E+    V  D + D
Sbjct: 75  AFDTESAGESEATGFVVDKKLGYILTNRHVVAPGPFVASAVFDNHEEIEIYPVYRDPVHD 134

Query: 158 LAVLKV--QSDRKFIPVEFEDANNI-RVGEAVFTIGNPFRLRGTVSAGIVSALDRDIPDR 214
               +    + R  I  E   A  + +VG  +  +GN    + ++ AG +S LDR+ PD 
Sbjct: 135 FGFFRYDPSTIRFSIVTEICLAPELAKVGSEIRVVGNDAGEKLSILAGFLSRLDRNAPDY 194

Query: 215 P-------GTF-TQIDAPINQGNSGGPCFNALGHVIGVNAMIVTSGQFHMGVGLIIPLSI 266
                    TF  Q  +  + G+SG P  +  G+ + +NA    S          +PL  
Sbjct: 195 GEDTYNDFNTFYIQAASSTSGGSSGSPVVDIPGYAVALNAGGSISS----ASDFFLPLDR 250

Query: 267 IKKAIPSLISKGRVDHGWFGIMTQNLTQELAIPLGLR------------GTKGSL-ITAV 313
           + +A+  L +   +  G   +   +   +    LGL                G L +  V
Sbjct: 251 VVRALRCLQNNTPITRGTLQVEFLHKLFDECRRLGLSSEWEQVVRTKFPERTGMLVVETV 310

Query: 314 VKESPADKAGMKVGDVICMLDGRIIKSHQDFVWQIASRSPKEQVKISLCKEGSKHSVAVV 373
           + E PA+K  ++ GD++  ++   +   +  + QI      + +++++ + G +  + V 
Sbjct: 311 LPEGPAEKK-LEPGDILLAVNSTCLNDFEA-LEQILDEGVGKNLELTIQRGGQELELTVT 368

Query: 374 LGSSPTAKNDMHLEVGDKELLGMVLQDIN 402
           +        D  LEV      G V  D++
Sbjct: 369 VQDLHGITPDRFLEVC-----GAVFHDLS 392


>gnl|CDD|29046 cd00989, PDZ_metalloprotease, PDZ domain of bacterial and plant
           zinc metalloprotases, presumably membrane-associated or
           integral membrane proteases, which may be involved in
           signalling and regulatory mechanisms. May be responsible
           for substrate recognition and/or binding, as most PDZ
           domains bind C-terminal polypeptides, and binding to
           internal (non-C-terminal) polypeptides and even to
           lipids has been demonstrated. In this subfamily of
           protease-associated PDZ domains a C-terminal beta-strand
           forms the peptide-binding groove base, a circular
           permutation with respect to PDZ domains found in
           Eumetazoan signaling proteins..
          Length = 79

 Score = 47.9 bits (114), Expect = 6e-06
 Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 303 RGTKGSLITAVVKESPADKAGMKVGDVICMLDGRIIKSHQDFVWQIASRSPKEQVKISLC 362
                 +I  VV  SPA KAG+K GD I  ++G+ IKS +D V  +   +P + + +++ 
Sbjct: 9   GPPIEPVIGEVVPGSPAAKAGLKAGDRILAINGQKIKSWEDLVDAVQ-ENPGKPLTLTVE 67

Query: 363 KEGSKHSVAVV 373
           + G   ++ + 
Sbjct: 68  RNGETITLTLT 78



 Score = 27.5 bits (61), Expect = 8.1
 Identities = 8/54 (14%), Positives = 23/54 (42%), Gaps = 6/54 (11%)

Query: 423 EAKGIQKGMTIVSVNTHEVSCIKDVERLIGKAKEK------KRDSVLLQIKYDP 470
              G++ G  I+++N  ++   +D+   + +   K      +R+   + +   P
Sbjct: 26  AKAGLKAGDRILAINGQKIKSWEDLVDAVQENPGKPLTLTVERNGETITLTLTP 79


>gnl|CDD|29043 cd00986, PDZ_LON_protease, PDZ domain of ATP-dependent LON serine
           proteases. Most PDZ domains bind C-terminal
           polypeptides, though binding to internal
           (non-C-terminal) polypeptides and even to lipids has
           been demonstrated. In this bacterial subfamily of
           protease-associated PDZ domains a C-terminal beta-strand
            is thought to form the peptide-binding groove base, a
           circular permutation with respect to PDZ domains found
           in Eumetazoan signaling proteins..
          Length = 79

 Score = 43.0 bits (101), Expect = 2e-04
 Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 306 KGSLITAVVKESPADKAGMKVGDVICMLDGRIIKSHQDFVWQIASRSPKEQVKISLCKEG 365
            G  +T+VV+  PA    +K GD I  +DG+  K  ++ +  I S+   + VK+ + +E 
Sbjct: 8   HGVYVTSVVEGMPA-AGKLKAGDHIIAVDGKPFKEAEELIDYIQSKKEGDTVKLKVKREE 66

Query: 366 SKHSVAVVLGSSP 378
            +    ++L + P
Sbjct: 67  KELPEDLILKTFP 79


>gnl|CDD|29047 cd00990, PDZ_glycyl_aminopeptidase, PDZ domain associated with
           archaeal and bacterial M61 glycyl-aminopeptidases. May
           be responsible for substrate recognition and/or binding,
           as most PDZ domains bind C-terminal polypeptides, and
           binding to internal (non-C-terminal) polypeptides and
           even to lipids has been demonstrated. In this subfamily
           of protease-associated PDZ domains a C-terminal
           beta-strand is presumed to form the peptide-binding
           groove base, a circular permutation with respect to PDZ
           domains found in Eumetazoan signaling proteins..
          Length = 80

 Score = 38.4 bits (89), Expect = 0.004
 Identities = 17/67 (25%), Positives = 35/67 (52%), Gaps = 3/67 (4%)

Query: 310 ITAVVKESPADKAGMKVGDVICMLDGRIIKSHQDFVWQIASRSPKEQVKISLCKEGSKHS 369
           +T V  +SPADKAG+  GD +  ++G  + + QD   ++      + V++++ ++     
Sbjct: 16  VTFVRDDSPADKAGLVAGDELVAVNGWRVDALQD---RLKEYQAGDPVELTVFRDDRLIE 72

Query: 370 VAVVLGS 376
           V + L  
Sbjct: 73  VPLTLAD 79


>gnl|CDD|29048 cd00991, PDZ_archaeal_metalloprotease, PDZ domain of archaeal zinc
           metalloprotases, presumably membrane-associated or
           integral membrane proteases, which may be involved in
           signalling and regulatory mechanisms. May be responsible
           for substrate recognition and/or binding, as most PDZ
           domains bind C-terminal polypeptides, and binding to
           internal (non-C-terminal) polypeptides and even to
           lipids has been demonstrated. In this subfamily of
           protease-associated PDZ domains a C-terminal beta-strand
           forms the peptide-binding groove base, a circular
           permutation with respect to PDZ domains found in
           Eumetazoan signaling proteins..
          Length = 79

 Score = 37.2 bits (86), Expect = 0.011
 Identities = 18/63 (28%), Positives = 34/63 (53%)

Query: 307 GSLITAVVKESPADKAGMKVGDVICMLDGRIIKSHQDFVWQIASRSPKEQVKISLCKEGS 366
           G +I  V+  SPA+ A +  GDVI  ++G  I + +DF+  +    P E + +++    +
Sbjct: 11  GVVIVGVIVGSPAENAVLHTGDVIYSINGTPITTLEDFMEALKPTKPGEVITVTVLPSTT 70

Query: 367 KHS 369
           K +
Sbjct: 71  KLT 73



 Score = 29.1 bits (65), Expect = 2.8
 Identities = 8/42 (19%), Positives = 18/42 (42%)

Query: 423 EAKGIQKGMTIVSVNTHEVSCIKDVERLIGKAKEKKRDSVLL 464
           E   +  G  I S+N   ++ ++D    +   K  +  +V +
Sbjct: 24  ENAVLHTGDVIYSINGTPITTLEDFMEALKPTKPGEVITVTV 65


>gnl|CDD|29049 cd00992, PDZ_signaling, PDZ domain found in a variety of Eumetazoan
           signaling molecules, often in tandem arrangements. May
           be responsible for specific protein-protein
           interactions, as most PDZ domains bind C-terminal
           polypeptides, and binding to internal (non-C-terminal)
           polypeptides and even to lipids has been demonstrated.
           In this subfamily of PDZ domains an N-terminal
           beta-strand forms the peptide-binding groove base, a
           circular permutation with respect to PDZ domains found
           in proteases..
          Length = 82

 Score = 37.1 bits (86), Expect = 0.011
 Identities = 13/61 (21%), Positives = 30/61 (49%), Gaps = 2/61 (3%)

Query: 301 GLRGTKGSLITAVVKESPADKAGMKVGDVICMLDGRII--KSHQDFVWQIASRSPKEQVK 358
           G     G  ++ V    PA++ G++VGD I  ++G  +   +H++ V  + +   +  + 
Sbjct: 21  GKDSGGGIFVSRVEPGGPAERGGLRVGDRILEVNGVSVEGLTHEEAVELLKNSGDEVTLT 80

Query: 359 I 359
           +
Sbjct: 81  V 81


>gnl|CDD|29042 cd00136, PDZ, PDZ domain, also called DHR (Dlg homologous region)
           or GLGF (after a conserved sequence motif). Many PDZ
           domains bind C-terminal polypeptides, though binding to
           internal (non-C-terminal) polypeptides and even to
           lipids has been demonstrated. Heterodimerization through
           PDZ-PDZ domain interactions adds to the domain's
           versatility, and PDZ domain-mediated interactions may be
           modulated dynamically through target phosphorylation.
           Some PDZ domains play a role in scaffolding
           supramolecular complexes. PDZ domains are found in
           diverse signaling proteins in bacteria, archebacteria,
           and eurkayotes. This CD contains two distinct structural
           subgroups with either a N- or C-terminal beta-strand
           forming the peptide-binding groove base. The circular
           permutation placing the strand on the N-terminus appears
           to be found in Eumetazoa only, while the C-terminal
           variant is found in all three kingdoms of life, and
           seems to co-occur with protease domains. PDZ domains
           have been named after PSD95(post synaptic density
           protein), DlgA (Drosophila disc large tumor suppressor),
           and ZO1, a mammalian tight junction protein..
          Length = 70

 Score = 37.1 bits (86), Expect = 0.011
 Identities = 17/68 (25%), Positives = 35/68 (51%), Gaps = 5/68 (7%)

Query: 299 PLGLRGTK----GSLITAVVKESPADKAGMKVGDVICMLDGRIIKSHQDFVW-QIASRSP 353
            LG         G ++ +V   SPA++AG++ GDVI  ++G  +K+       ++  +  
Sbjct: 2   GLGFSIRGGTEGGVVVLSVEPGSPAERAGLQAGDVILAVNGTDVKNLTLEDVAELLKKEV 61

Query: 354 KEQVKISL 361
            E+V +++
Sbjct: 62  GEKVTLTV 69


>gnl|CDD|33755 COG3975, COG3975, Predicted protease with the C-terminal PDZ domain
           [General function prediction only].
          Length = 558

 Score = 35.7 bits (82), Expect = 0.027
 Identities = 24/85 (28%), Positives = 37/85 (43%), Gaps = 11/85 (12%)

Query: 300 LGLR---GTKGSLITAVVKESPADKAGMKVGDVICMLDGRIIKSHQDFVWQIASRSPKEQ 356
           LGL+         IT V    PA KAG+  GD I  ++G           Q+      ++
Sbjct: 453 LGLKVKSEGGHEKITFVFPGGPAYKAGLSPGDKIVAING--------ISDQLDRYKVNDK 504

Query: 357 VKISLCKEGSKHSVAVVLGSSPTAK 381
           +++ + +EG      V LG  PTA+
Sbjct: 505 IQVHVFREGRLREFLVKLGGDPTAQ 529


>gnl|CDD|31136 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
           membrane].
          Length = 406

 Score = 35.3 bits (81), Expect = 0.037
 Identities = 14/32 (43%), Positives = 20/32 (62%)

Query: 305 TKGSLITAVVKESPADKAGMKVGDVICMLDGR 336
             G  + + +  SPA KAG+K GDVI  +DG+
Sbjct: 111 IGGVKVVSPIDGSPAAKAGIKPGDVIIKIDGK 142


>gnl|CDD|29045 cd00988, PDZ_CTP_protease, PDZ domain of C-terminal processing-,
           tail-specific-, and tricorn proteases, which function in
           posttranslational protein processing, maturation, and
           disassembly or degradation, in Bacteria, Archaea, and
           plant chloroplasts. May be responsible for substrate
           recognition and/or binding, as most PDZ domains bind
           C-terminal polypeptides, and binding to internal
           (non-C-terminal) polypeptides and even to lipids has
           been demonstrated. In this subfamily of
           protease-associated PDZ domains a C-terminal beta-strand
           forms the peptide-binding groove base, a circular
           permutation with respect to PDZ domains found in
           Eumetazoan signaling proteins..
          Length = 85

 Score = 34.8 bits (80), Expect = 0.047
 Identities = 16/31 (51%), Positives = 22/31 (70%)

Query: 306 KGSLITAVVKESPADKAGMKVGDVICMLDGR 336
            G +IT+V+  SPA KAG+K GD+I  +DG 
Sbjct: 13  GGLVITSVLPGSPAAKAGIKAGDIIVAIDGE 43


>gnl|CDD|144258 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF).  PDZ
           domains are found in diverse signaling proteins.
          Length = 80

 Score = 33.8 bits (78), Expect = 0.11
 Identities = 12/55 (21%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 306 KGSLITAVVKESPADKAGMKVGDVICMLDGRIIKSH-QDFVWQIASRSPKEQVKI 359
            G  ++ V+    A+  G++VGD I  ++G+ +++   D    +A +    +V +
Sbjct: 24  PGIFVSEVLPGGAAEAGGLQVGDRILSINGQDLENMSHDEA-VLALKGSGGEVTL 77


>gnl|CDD|38740 KOG3532, KOG3532, KOG3532, Predicted protein kinase [General
           function prediction only].
          Length = 1051

 Score = 32.0 bits (72), Expect = 0.36
 Identities = 12/50 (24%), Positives = 22/50 (44%)

Query: 293 TQELAIPLGLRGTKGSLITAVVKESPADKAGMKVGDVICMLDGRIIKSHQ 342
           +  + +       +   +  V   S ADKA  K GDV+  ++   I+S +
Sbjct: 385 SSPIGLVFDKNTNRAVKVCTVEDNSLADKAAFKPGDVLVAINNVPIRSER 434


>gnl|CDD|33283 COG3480, SdrC, Predicted secreted protein containing a PDZ domain
           [Signal transduction mechanisms].
          Length = 342

 Score = 31.8 bits (72), Expect = 0.38
 Identities = 15/67 (22%), Positives = 30/67 (44%), Gaps = 1/67 (1%)

Query: 306 KGSLITAVVKESPADKAGMKVGDVICMLDGRIIKSHQDFVWQIASRSPKEQVKISLCKEG 365
            G  + +V+  SP  K  ++ GD I  +DG    S  + +  ++S+ P ++V I   +  
Sbjct: 130 AGVYVLSVIDNSPF-KGKLEAGDTIIAVDGEPFTSSDELIDYVSSKKPGDEVTIDYERHN 188

Query: 366 SKHSVAV 372
               +  
Sbjct: 189 ETPEIVT 195


>gnl|CDD|38339 KOG3129, KOG3129, KOG3129, 26S proteasome regulatory complex,
           subunit PSMD9 [Posttranslational modification, protein
           turnover, chaperones].
          Length = 231

 Score = 31.5 bits (71), Expect = 0.59
 Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 2/66 (3%)

Query: 310 ITAVVKESPADKAGMKVGDVICMLDGRIIKSHQDF--VWQIASRSPKEQVKISLCKEGSK 367
           + +VV  SPAD+AG+ VGD I         +      +  +   +  + V +++ +EG K
Sbjct: 143 VDSVVPGSPADEAGLCVGDEILKFGNVHSGNFLPLQNIAAVVQSNEDQIVSVTVIREGQK 202

Query: 368 HSVAVV 373
             +++ 
Sbjct: 203 VVLSLT 208


>gnl|CDD|36323 KOG1107, KOG1107, KOG1107, Membrane coat complex Retromer, subunit
           VPS35 [Intracellular trafficking, secretion, and
           vesicular transport].
          Length = 760

 Score = 29.9 bits (67), Expect = 1.7
 Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 6/70 (8%)

Query: 397 VLQDINDGNKKLVRIVALNPNREREVEAKGIQKGMTIVSVNTHEVSCIKDVERLIGKAKE 456
           VL +  + NK  VR+    P+RE+E   K   +   +V  N   +S      +L G   E
Sbjct: 153 VLINFTEMNKLWVRMQHQGPSREKEKREKERNELRILVGKNLVRLS------QLEGVDLE 206

Query: 457 KKRDSVLLQI 466
             RD VL +I
Sbjct: 207 MYRDDVLPRI 216


>gnl|CDD|38761 KOG3553, KOG3553, KOG3553, Tax interaction protein TIP1 [Cell
           wall/membrane/envelope biogenesis].
          Length = 124

 Score = 28.9 bits (64), Expect = 3.0
 Identities = 12/30 (40%), Positives = 20/30 (66%)

Query: 306 KGSLITAVVKESPADKAGMKVGDVICMLDG 335
           KG  +T V + SPA+ AG+++ D I  ++G
Sbjct: 59  KGIYVTRVSEGSPAEIAGLRIHDKILQVNG 88


>gnl|CDD|31349 COG1155, NtpA, Archaeal/vacuolar-type H+-ATPase subunit A [Energy
           production and conversion].
          Length = 588

 Score = 29.1 bits (65), Expect = 3.3
 Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 10/73 (13%)

Query: 160 VLKVQSDRKFIPVEFEDANNIRVGEAVFTIGNPFR------LRGTVSAGIVSALDRDIPD 213
           +++++ +R  I V +ED   IR GE V   G P        L  ++  GI   LD  I +
Sbjct: 38  IIRIEGNRATIQV-YEDTAGIRPGEKVENTGRPLSVELGPGLLKSIYDGIQRPLDV-IKE 95

Query: 214 RPGTFTQ--IDAP 224
             G F    ++ P
Sbjct: 96  TSGDFIARGLNPP 108


>gnl|CDD|32719 COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell
           division and chromosome partitioning].
          Length = 272

 Score = 28.2 bits (63), Expect = 5.0
 Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 16/71 (22%)

Query: 426 GIQKGMTI--------VSVNTHEVSCIKDVERLIG--------KAKEKKRDSVLLQIKYD 469
           GI++G           + V   EVS ++D +R+IG            ++    LL  +Y 
Sbjct: 124 GIEQGFKNAVYFADEAIVVTNPEVSSVRDSDRIIGLLESKSRRAEIGEEPKEHLLLNRYR 183

Query: 470 PDMQSGNDNMS 480
           P+M    + +S
Sbjct: 184 PEMVKRGEMLS 194


>gnl|CDD|88595 cd05795, Ribosomal_P0_L10e, Ribosomal protein L10 family, P0 and
           L10e subfamily; composed of eukaryotic 60S ribosomal
           protein P0 and the archaeal P0 homolog, L10e. P0 or L10e
           forms a tight complex with multiple copies of the small
           acidic protein L12(e). This complex forms a stalk
           structure on the large subunit of the ribosome. The
           stalk is known to contain the binding site for
           elongation factors G and Tu (EF-G and EF-Tu,
           respectively); however, there is disagreement as to
           whether or not L10 is involved in forming the binding
           site. The stalk is believed to be associated with GTPase
           activities in protein synthesis. In a neuroblastoma cell
           line, L10 has been shown to interact with the SH3 domain
           of Src and to activate the binding of the Nck1 adaptor
           protein with skeletal proteins such as the
           Wiskott-Aldrich Syndrome Protein (WASP) and the
           WASP-interacting protein (WIP). These eukaryotic and
           archaeal P0 sequences have an additional C-terminal
           domain homologous with acidic proteins P1 and P2..
          Length = 175

 Score = 28.2 bits (63), Expect = 5.5
 Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 5/46 (10%)

Query: 186 VFTIGNPFRLRGTVSAGIVSALDRDIPDRPGTFTQIDAPINQGNSG 231
           +FT G+PF +R  +    V A     P +PG     D  +  G +G
Sbjct: 82  IFTNGDPFEIRKILEENKVPA-----PAKPGAIAPCDVVVPAGPTG 122


>gnl|CDD|33306 COG3503, COG3503, Predicted membrane protein [Function unknown].
          Length = 323

 Score = 28.0 bits (62), Expect = 6.3
 Identities = 12/64 (18%), Positives = 24/64 (37%), Gaps = 4/64 (6%)

Query: 240 HVIGVNAMIVTSGQFHMGVGLIIPLSIIKKAIPSLISKGRVDHG---WFGIMTQNLTQEL 296
           H IG+ A ++ +    +   +++ L++   A   L+   R       W G+         
Sbjct: 121 HAIGL-ASLLGAAFLWLPRAVLLALAVAAVAAHILLRPARFGTPMLWWLGLRPYGPRTLD 179

Query: 297 AIPL 300
             PL
Sbjct: 180 YYPL 183


>gnl|CDD|31093 COG0750, COG0750, Predicted membrane-associated Zn-dependent
           proteases 1 [Cell envelope biogenesis, outer membrane].
          Length = 375

 Score = 27.8 bits (61), Expect = 7.0
 Identities = 12/54 (22%), Positives = 25/54 (46%)

Query: 309 LITAVVKESPADKAGMKVGDVICMLDGRIIKSHQDFVWQIASRSPKEQVKISLC 362
           ++  V  +S A  AG++ GD I  +DG  + S  D    + + +      +++ 
Sbjct: 132 VVGEVAPKSAAALAGLRPGDRIVAVDGEKVASWDDVRRLLVAAAGDVFNLLTIL 185


>gnl|CDD|34816 COG5219, COG5219, Uncharacterized conserved protein, contains RING
           Zn-finger [General function prediction only].
          Length = 1525

 Score = 27.8 bits (61), Expect = 7.2
 Identities = 13/83 (15%), Positives = 30/83 (36%), Gaps = 2/83 (2%)

Query: 82  LKNYFRKDFHKFFSGEEPILSDTVERLMFGSGFF--ITDDGYILTSNHIVEDGASFSVIL 139
           L   +      + + + PI  D   +L     F+  + D      +   V+ G  F  I+
Sbjct: 773 LVFSYDSLMEIYLTSDTPIALDLSNKLFIDQDFYYRLLDRVDEPINRPRVDVGTQFVHII 832

Query: 140 SDDTELPAKLVGTDALFDLAVLK 162
              + +  + +  D+ F    ++
Sbjct: 833 DYYSRILEEYLDGDSGFIRTFVE 855


>gnl|CDD|33956 COG4231, COG4231, Indolepyruvate ferredoxin oxidoreductase, alpha
           and beta subunits [Energy production and conversion].
          Length = 640

 Score = 27.6 bits (61), Expect = 8.8
 Identities = 19/97 (19%), Positives = 39/97 (40%), Gaps = 5/97 (5%)

Query: 368 HSVAVVLGSSPTAKNDMHLEVGDKELLGMVLQDINDGNKKLVRIVALNPNREREVEAKGI 427
           HS  + L ++   K ++ + V D     M     + G       VA    +   +  + +
Sbjct: 459 HSGILALINAVYNKANILVVVLDNRTTAMTGGQPHPG-----TGVAAEGTKSTAIVIEEV 513

Query: 428 QKGMTIVSVNTHEVSCIKDVERLIGKAKEKKRDSVLL 464
            + M +  V T +   +K++   I +A E    SV++
Sbjct: 514 VRAMGVEDVETVDPYDVKELSEAIKEALEVPGPSVII 550


>gnl|CDD|146618 pfam04083, Abhydro_lipase, ab-hydrolase associated lipase region. 
          Length = 62

 Score = 27.5 bits (62), Expect = 9.4
 Identities = 8/13 (61%), Positives = 10/13 (76%)

Query: 116 ITDDGYILTSNHI 128
            T+DGYILT + I
Sbjct: 18  TTEDGYILTLHRI 30


  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
   0.319    0.137    0.393 

Gapped
Lambda     K      H
   0.267   0.0810    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,727,819
Number of extensions: 308430
Number of successful extensions: 755
Number of sequences better than 10.0: 1
Number of HSP's gapped: 747
Number of HSP's successfully gapped: 38
Length of query: 489
Length of database: 6,263,737
Length adjustment: 98
Effective length of query: 391
Effective length of database: 4,146,055
Effective search space: 1621107505
Effective search space used: 1621107505
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.4 bits)