RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780801|ref|YP_003065214.1| hypothetical protein
CLIBASIA_03460 [Candidatus Liberibacter asiaticus str. psy62]
         (222 letters)



>gnl|CDD|143483 cd00635, PLPDE_III_YBL036c_like, Type III Pyridoxal 5-phosphate
           (PLP)-Dependent Enzymes, YBL036c-like proteins.  This
           family contains mostly uncharacterized proteins, widely
           distributed among eukaryotes, bacteria and archaea, that
           bear similarity to the yeast hypothetical protein
           YBL036c, which is homologous to a Pseudomonas aeruginosa
           gene that is co-transcribed with a known proline
           biosynthetic gene. YBL036c is a single domain monomeric
           protein with a typical TIM barrel fold. It binds the PLP
           cofactor and has been shown to exhibit amino acid
           racemase activity. The YBL036c structure is similar to
           the N-terminal domain of the fold type III PLP-dependent
           enzymes, bacterial alanine racemase and eukaryotic
           ornithine decarboxylase, which are two-domain dimeric
           proteins. The lack of a second domain in YBL036c may
           explain limited D- to L-alanine racemase or non-specific
           racemase activity.
          Length = 222

 Score =  241 bits (618), Expect = 1e-64
 Identities = 89/215 (41%), Positives = 122/215 (56%), Gaps = 10/215 (4%)

Query: 11  KQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKWIPLRK 70
           +++I  +A  A R  D V+LVAVSK V ++ IR A+  GQ  F EN++QEA  K      
Sbjct: 9   RERIAAAAERAGRDPDEVTLVAVSKTVPAEAIREAIEAGQRDFGENRVQEALDKA-EELP 67

Query: 71  EWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGY 130
           + D++  FIG LQ+NKV   V LFD+I +V   K A  L+    K+ R L V +QVN G 
Sbjct: 68  DPDIEWHFIGHLQTNKVKYAVRLFDLIHSVDSLKLAEELNKRAEKEGRVLDVLVQVNIGG 127

Query: 131 EIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPK---PHFYLLSEIARECK-- 185
           E  KSG+ P + ++ +        L + GLM I P   +P+   P+F  L E+  E    
Sbjct: 128 EESKSGVAPEELEELLEEIAALPNLRIRGLMTIAPLTEDPEEVRPYFRELRELRDELGAK 187

Query: 186 ----LTKLSMGMTRDFELAIASGATSVRIGSGIFG 216
               L +LSMGM+ DFE+AI  GAT VRIG+ IFG
Sbjct: 188 GGVNLKELSMGMSGDFEIAIEEGATLVRIGTAIFG 222


>gnl|CDD|30673 COG0325, COG0325, Predicted enzyme with a TIM-barrel fold [General
           function prediction only].
          Length = 228

 Score =  220 bits (562), Expect = 3e-58
 Identities = 86/227 (37%), Positives = 124/227 (54%), Gaps = 8/227 (3%)

Query: 1   MSLGNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQE 60
           M +   L   +++I  +A  A R   SV+LVAVSK V ++ IR A   GQ  F EN++QE
Sbjct: 1   MDIKENLAAVRERIAAAAERAGRNPGSVTLVAVSKTVPAEDIREAYEAGQRHFGENRVQE 60

Query: 61  AKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFL 120
           A  K   L+   D++  FIG LQSNKV  +   FD I ++ R K A  L+   ++  + L
Sbjct: 61  ALDKIEALKDLPDIEWHFIGPLQSNKVKLVAENFDWIHSLDRLKLAKELNKRALELPKPL 120

Query: 121 PVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPHFYLLSEI 180
            V IQVN   E  KSG+ P +  +     ++   L + GLM IPP   +P+  F +  ++
Sbjct: 121 NVLIQVNISGEESKSGVPPEELDELAQEVQELPNLELRGLMTIPPLTDDPEEIFAVFRKL 180

Query: 181 A--------RECKLTKLSMGMTRDFELAIASGATSVRIGSGIFGERP 219
                    +   + +LSMGM+ D+E+AIA GAT VRIG+ IFG R 
Sbjct: 181 RKLFDELKAKYPPIDELSMGMSNDYEIAIAEGATMVRIGTAIFGARD 227


>gnl|CDD|143497 cd06824, PLPDE_III_Yggs_like, Pyridoxal 5-phosphate (PLP)-binding
           TIM barrel domain of Type III PLP-Dependent Enzymes,
           Yggs-like proteins.  This subfamily contains mainly
           uncharacterized proteobacterial proteins with similarity
           to the hypothetical Escherichia coli protein YggS, a
           homolog of yeast YBL036c, which is homologous to a
           Pseudomonas aeruginosa gene that is co-transcribed with
           a known proline biosynthetic gene. Like yeast YBL036c,
           Yggs is a single domain monomeric protein with a typical
           TIM-barrel fold. Its structure, which shows a
           covalently-bound PLP cofactor, is similar to the
           N-terminal domain of the fold type III PLP-dependent
           enzymes, bacterial alanine racemase and eukaryotic
           ornithine decarboxylase, which are two-domain dimeric
           proteins. YggS has not been characterized extensively
           and its biological function is still unkonwn.
          Length = 224

 Score =  167 bits (426), Expect = 2e-42
 Identities = 85/224 (37%), Positives = 112/224 (50%), Gaps = 8/224 (3%)

Query: 2   SLGNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEA 61
           ++   L   KQ+I  +A  A R   SV L+AVSK   +  IR A + GQ  F EN +QEA
Sbjct: 1   NIAENLAQVKQRIAQAAKQAGRDPSSVQLLAVSKTKPADAIREAYAAGQRHFGENYVQEA 60

Query: 62  KKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLP 121
            +K   LR   D++  FIG +QSNK   I   FD + +V R K A  L+ +       L 
Sbjct: 61  LEKIEALRDLQDIEWHFIGPIQSNKTKLIAENFDWVHSVDRLKIAKRLNDQRPAGLPPLN 120

Query: 122 VYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPA---MGNPKPHFYLLS 178
           V IQVN   E  KSG+ P    +      Q   L + GLM IP         +  F  L 
Sbjct: 121 VCIQVNISGEDSKSGVAPEDAAELAEAISQLPNLRLRGLMAIPAPTDDEAAQRAAFKRLR 180

Query: 179 EIARECK-----LTKLSMGMTRDFELAIASGATSVRIGSGIFGE 217
           ++  + K     L  LSMGM+ D E AIA+G+T VRIG+ IFG 
Sbjct: 181 QLFDQLKKQYPDLDTLSMGMSGDLEAAIAAGSTMVRIGTAIFGA 224


>gnl|CDD|143496 cd06822, PLPDE_III_YBL036c_euk, Pyridoxal 5-phosphate (PLP)-binding
           TIM barrel domain of Type III PLP-Dependent Enzymes,
           Eukaryotic YBL036c-like proteins.  This subfamily
           contains mostly uncharacterized eukaryotic proteins with
            similarity to the yeast hypothetical protein YBL036c,
           which is homologous to a Pseudomonas aeruginosa gene
           that is co-transcribed with a known proline biosynthetic
           gene. YBL036c is a single domain monomeric protein with
           a typical TIM barrel fold. It binds the PLP cofactor and
           has been shown to exhibit amino acid racemase activity.
           The YBL036c structure is similar to the N-terminal
           domain of the fold type III PLP-dependent enzymes,
           bacterial alanine racemase and eukaryotic ornithine
           decarboxylase, which are two-domain dimeric proteins.
           The lack of a second domain in YBL036c may explain
           limited D- to L-alanine racemase or non-specific
           racemase activity. Some members of this subfamily are
           also referred to as PROSC (Proline synthetase
           co-transcribed bacterial homolog).
          Length = 227

 Score =  136 bits (345), Expect = 4e-33
 Identities = 81/225 (36%), Positives = 118/225 (52%), Gaps = 25/225 (11%)

Query: 11  KQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKWIPLRK 70
           +Q ++ ++   K P     LVAVSK   ++ I+ A   GQ  F EN +QE  +K   L  
Sbjct: 9   RQAVKRAS--KKLPASKPRLVAVSKTKPAELIKEAYDAGQRHFGENYVQELIEKAPDLPI 66

Query: 71  EWDVQLRFIGSLQSNKVSEIVS---LFDVIETVSREKTASLL--SLEMIKQSRFLPVYIQ 125
             D++  FIG LQSNKV +++    L+ ++ETV  EK A  L  + E + +   L V +Q
Sbjct: 67  --DIKWHFIGHLQSNKVKKLLKVPNLY-MVETVDSEKLADKLNKAWEKLGEREPLKVMVQ 123

Query: 126 VNTGYEIQKSGIMPNQTKDFVILCRQKYQ-LNVEGLMCIPPAMGN-----PKPHFYLLSE 179
           VNT  E  KSG+ P++  + V    ++   L   GLM I  + G      P P F  L +
Sbjct: 124 VNTSGEESKSGLEPSEAVELVKHIIEECPNLKFSGLMTIG-SFGYSLSSGPNPDFLCLVD 182

Query: 180 IARE-CKLTK-------LSMGMTRDFELAIASGATSVRIGSGIFG 216
             ++ C+          LSMGM+ DFE AI  G+T+VR+GS IFG
Sbjct: 183 CRKKVCEKLGINPDDLELSMGMSADFEHAIEMGSTNVRVGSAIFG 227


>gnl|CDD|38367 KOG3157, KOG3157, KOG3157, Proline synthetase co-transcribed
           protein [General function prediction only].
          Length = 244

 Score =  129 bits (325), Expect = 7e-31
 Identities = 81/233 (34%), Positives = 115/233 (49%), Gaps = 19/233 (8%)

Query: 4   GNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKK 63
            + L+   ++++ +     R +++V LVAVSK   +  I  A   GQ  F EN +QE  +
Sbjct: 8   ASALRAVIERVQQAVNQRPRDENAVRLVAVSKTKPASLIIEAYDAGQRHFGENYVQELIE 67

Query: 64  KWIPLRKEWDVQLRFIGSLQSNKVSEI--VSLFDVIETVSREKTASLLSLEMIKQSRFLP 121
           K  PL  + D++  FIG LQSNK  ++  V     +ETV  EK A  L     K     P
Sbjct: 68  K-APLLPD-DIKWHFIGHLQSNKCKKLLSVPNLYSVETVDSEKKARKLDSAWSKLGPDNP 125

Query: 122 --VYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQ-LNVEGLMCIPPA----MGNPKPHF 174
             V +QVNT  E  KSGI P++  +     + + + L   GLM I            P F
Sbjct: 126 LKVLVQVNTSGEDSKSGIEPSEAPELAEHIKSECKNLKFSGLMTIGSFDNSHSSGENPDF 185

Query: 175 YLLSEIARE-CKLT-------KLSMGMTRDFELAIASGATSVRIGSGIFGERP 219
            +L ++    CK         +LSMGM+ DF LAI  G+T+VR+GS IFG R 
Sbjct: 186 QVLVKLRESICKKLGIPADQVELSMGMSADFLLAIEQGSTNVRVGSTIFGARE 238


>gnl|CDD|144675 pfam01168, Ala_racemase_N, Alanine racemase, N-terminal domain. 
          Length = 216

 Score =  116 bits (294), Expect = 3e-27
 Identities = 56/217 (25%), Positives = 85/217 (39%), Gaps = 20/217 (9%)

Query: 15  ENSAILAKRPKDSVSLVAVSKM----VDSKKIRVALSCGQVIFAENKLQEAKKKWIPLRK 70
            N   L +R    V L+AV K       + ++  AL+ G   F    LQEA    + LR+
Sbjct: 8   HNIRALRERAGRPVKLMAVVKANAYGHGAVRVARALAAGADGFGVATLQEA----LELRE 63

Query: 71  E-WDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTG 129
                 +  +G     +++     +D+I TV   + A  LS    K  R L V+++V+TG
Sbjct: 64  AGITAPILVLGFFPPEELALAAE-YDLIPTVDSLEQAEALSAAAAKLGRPLRVHLKVDTG 122

Query: 130 YEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNP----KPHFYLLSEIAR--E 183
               + G  P +             L +EGLM        P    +       E+A   E
Sbjct: 123 MG--RLGFTPEELPALAEALALP-GLRLEGLMTHFACADEPDATNRAQLARFRELADALE 179

Query: 184 CKLTKLSMGMTRDFELAI-ASGATSVRIGSGIFGERP 219
                LS+G +    LA    G   VR G  ++G RP
Sbjct: 180 AAGPVLSLGNSAALLLAPLHEGFDMVRPGIALYGARP 216


>gnl|CDD|143484 cd06808, PLPDE_III, Type III Pyridoxal 5-phosphate (PLP)-Dependent
           Enzymes.  The fold type III PLP-dependent enzyme family
           is predominantly composed of two-domain proteins with
           similarity to bacterial alanine racemases (AR) including
           eukaryotic ornithine decarboxylases (ODC), prokaryotic
           diaminopimelate decarboxylases (DapDC), biosynthetic
           arginine decarboxylases (ADC), carboxynorspermidine
           decarboxylases (CANSDC), and similar proteins. AR-like
           proteins contain an N-terminal PLP-binding TIM-barrel
           domain and a C-terminal beta-sandwich domain. They exist
           as homodimers with active sites that lie at the
           interface between the TIM barrel domain of one subunit
           and the beta-sandwich domain of the other subunit. These
           proteins play important roles in the biosynthesis of
           amino acids and polyamine. The family also includes the
           single-domain YBL036c-like proteins, which contain a
           single PLP-binding TIM-barrel domain without any N- or
           C-terminal extensions. Due to the lack of a second
           domain, these proteins may possess only limited D- to
           L-alanine racemase activity or non-specific racemase
           activity.
          Length = 211

 Score = 33.4 bits (77), Expect = 0.047
 Identities = 16/82 (19%), Positives = 34/82 (41%)

Query: 83  QSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQT 142
           Q +++ +      ++ TV   +    L    +K      V ++++TG E  K G+ P + 
Sbjct: 70  QVSELEDAAEQGVIVVTVDSLEELEKLEEAALKAGPPARVLLRIDTGDENGKFGVRPEEL 129

Query: 143 KDFVILCRQKYQLNVEGLMCIP 164
           K  +   ++   L + GL    
Sbjct: 130 KALLERAKELPHLRLVGLHTHF 151


>gnl|CDD|143481 cd00430, PLPDE_III_AR, Type III Pyridoxal 5-phosphate
           (PLP)-Dependent Enzyme Alanine Racemase.  This family
           includes predominantly bacterial alanine racemases (AR),
           some serine racemases (SerRac), and putative
           bifunctional enzymes containing N-terminal
           UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine
           ligase (murF) and C-terminal AR domains. These proteins
           are fold type III PLP-dependent enzymes that play
           essential roles in peptidoglycan biosynthesis. AR
           catalyzes the interconversion between L- and D-alanine,
           which is an essential component of the peptidoglycan
           layer of bacterial cell walls. SerRac converts L-serine
           into its D-enantiomer (D-serine) for peptidoglycan
           synthesis. murF catalyzes the addition of D-Ala-D-Ala to
           UDPMurNAc-tripeptide, the final step in the synthesis of
           the cytoplasmic precursor of bacterial cell wall
           peptidoglycan. Members of this family contain an
           N-terminal PLP-binding TIM-barrel domain and a
           C-terminal beta-sandwich domain. They exist as
           homodimers with active sites that lie at the interface
           between the TIM barrel domain of one subunit and the
           beta-sandwich domain of the other subunit. AR and other
           members of this family require dimer formation and the
           presence of the PLP cofactor for catalytic activity.
           Fungal ARs and eukaryotic serine racemases, which are
           fold types I and II PLP-dependent enzymes respectively,
           are excluded from this family.
          Length = 367

 Score = 33.2 bits (77), Expect = 0.050
 Identities = 16/68 (23%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 94  FDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKY 153
           +D+  TVS  + A  LS    +  + L V+++++TG  + + G  P + ++ +   +   
Sbjct: 93  YDLTPTVSSLEQAEALSAAAARLGKTLKVHLKIDTG--MGRLGFRPEEAEELLEALKALP 150

Query: 154 QLNVEGLM 161
            L +EG+ 
Sbjct: 151 GLELEGVF 158


>gnl|CDD|31130 COG0787, Alr, Alanine racemase [Cell envelope biogenesis, outer
           membrane].
          Length = 360

 Score = 32.9 bits (75), Expect = 0.080
 Identities = 13/73 (17%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 89  EIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVIL 148
           E+ + +++   V+  +    L      +++ L V+++++TG  + + G+ P +     I 
Sbjct: 92  ELAAAYNLTPVVNSLEQLEALK-NAALKNKPLKVHLKIDTG--MNRLGLRPEEAVALAID 148

Query: 149 CRQKYQLNVEGLM 161
                 L++EG+ 
Sbjct: 149 LIALKNLDLEGIF 161


>gnl|CDD|143495 cd06821, PLPDE_III_D-TA, Type III Pyridoxal 5-phosphate
           (PLP)-Dependent Enzyme D-Threonine Aldolase.
           D-threonine aldolase (D-TA, EC 4.3.1.18) reversibly
           catalyzes the aldol cleavage of D-threonine into glycine
           and acetaldehyde, and the synthesis of D-threonine from
           glycine and acetaldehyde. Its activity is present in
           several genera of bacteria but not in fungi. It requires
           PLP and a divalent cation such as Co2+, Ni2+, Mn2+, or
           Mg2+ as cofactors for catalytic activity and thermal
           stability. Members of this subfamily show similarity to
           bacterial alanine racemase (AR), a fold type III
           PLP-dependent enzyme which contains an N-terminal
           PLP-binding TIM-barrel domain and a C-terminal
           beta-sandwich domain. AR exists as homodimers with
           active sites that lie at the interface between the TIM
           barrel domain of one subunit and the beta-sandwich
           domain of the other subunit. Based on its similarity to
           AR, it is possible that low specificity D-TAs also form
           dimers in solution. Experimental data show that the
           monomeric form of low specificity D-TAs exhibit full
           catalytic activity.
          Length = 361

 Score = 30.3 bits (69), Expect = 0.39
 Identities = 15/59 (25%), Positives = 22/59 (37%), Gaps = 3/59 (5%)

Query: 105 TASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTK-DFVILCRQKYQLNVEGLMC 162
            A  LS         L V + VNTG  + ++GI P +   +          L + GL  
Sbjct: 114 AAEALSAAAGSAGLTLSVLLDVNTG--MNRTGIAPGEDAEELYRAIATLPGLVLAGLHA 170


>gnl|CDD|163674 cd03174, DRE_TIM_metallolyase, DRE-TIM metallolyase superfamily.
           The DRE-TIM metallolyase superfamily includes
           2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
           synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
           homocitrate synthase, citramalate synthase,
           4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
           transcarboxylase 5S, pyruvate carboxylase, AksA, and
           FrbC.  These members all share a conserved
           triose-phosphate isomerase (TIM) barrel domain
           consisting of a core beta(8)-alpha(8) motif with the
           eight parallel beta strands forming an enclosed barrel
           surrounded by eight alpha helices.  The domain has a
           catalytic center containing a divalent cation-binding
           site formed by a cluster of invariant residues that cap
           the core of the barrel.  In addition, the catalytic site
           includes three invariant residues - an aspartate (D), an
           arginine (R), and a glutamate (E) - which is the basis
           for the domain name "DRE-TIM".
          Length = 265

 Score = 29.0 bits (66), Expect = 1.0
 Identities = 10/37 (27%), Positives = 14/37 (37%), Gaps = 3/37 (8%)

Query: 177 LSEIARECKLTKLSM---GMTRDFELAIASGATSVRI 210
           L  I +     KL        +  E A+ +G   VRI
Sbjct: 57  LRAIRKLVPNVKLQALVRNREKGIERALEAGVDEVRI 93


>gnl|CDD|143490 cd06815, PLPDE_III_AR_like_1, Type III Pyridoxal 5-phosphate
           (PLP)-Dependent Enzyme Alanine Racemase-like 1.  This
           subfamily is composed of uncharacterized bacterial
           proteins with similarity to bacterial alanine racemases
           (AR), which are fold type III PLP-dependent enzymes
           containing an N-terminal PLP-binding TIM-barrel domain
           and a C-terminal beta-sandwich domain. AR exists as
           homodimers with active sites that lie at the interface
           between the TIM barrel domain of one subunit and the
           beta-sandwich domain of the other subunit. It catalyzes
           the interconversion between L- and D-alanine, which is
           an essential component of the peptidoglycan layer of
           bacterial cell walls. Members of this subfamily may act
           as PLP-dependent enzymes.
          Length = 353

 Score = 28.7 bits (65), Expect = 1.4
 Identities = 54/243 (22%), Positives = 91/243 (37%), Gaps = 55/243 (22%)

Query: 6   KLQVFKQKIENSA-ILAKRPKDS-VSLVAVSKMV--DSKKIRVALSCGQVIFAENKLQEA 61
           +L++   KI ++A +L +  K   + +  V+K+V  D +     L  G    A+++++  
Sbjct: 3   RLEINLSKIRHNAKVLVELCKSRGIEVTGVTKVVCGDPEIAEALLEGGITHLADSRIENL 62

Query: 62  KK---------KW---IPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLL 109
           KK         K    IP+  E               V ++V   D+    S  +T   L
Sbjct: 63  KKLKDLGISGPKMLLRIPMLSE---------------VEDVVKYADIS-LNSELETIKAL 106

Query: 110 SLEMIKQSRFLPVYIQVNTG--YEIQKSGIMPNQTKDFVILCRQKYQLNVEG----LMCI 163
           S E  KQ +   + + V+ G   E    G++P    DFV    +   + + G    L C 
Sbjct: 107 SEEAKKQGKIHKIILMVDLGDLRE----GVLPEDLLDFVEEILKLPGIELVGIGTNLGCY 162

Query: 164 PPAMGNPKPH-FYLLSEIARE------CKLTKLSMGMTRDFELA----IASGATSVRIGS 212
              +  P       L E+  E       KL  +S G +    L     +  G   +RIG 
Sbjct: 163 GGVL--PTEENMGKLVELKEEIEKEFGIKLPIISGGNSASLPLLLKGELPGGINQLRIGE 220

Query: 213 GIF 215
            I 
Sbjct: 221 AIL 223


>gnl|CDD|36634 KOG1420, KOG1420, KOG1420, Ca2+-activated K+ channel Slowpoke,
           alpha subunit [Inorganic ion transport and metabolism,
           Signal transduction mechanisms].
          Length = 1103

 Score = 28.1 bits (62), Expect = 1.9
 Identities = 13/46 (28%), Positives = 27/46 (58%), Gaps = 1/46 (2%)

Query: 66  IPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSL 111
           I L + W + LRF+ +L+   V +I+   ++++T S  +   L+S+
Sbjct: 212 IYLNRSW-LGLRFLRALRLMTVPDILQYLNILKTSSSIRLVQLVSI 256


>gnl|CDD|30933 COG0588, GpmA, Phosphoglycerate mutase 1 [Carbohydrate transport
          and metabolism].
          Length = 230

 Score = 28.3 bits (63), Expect = 2.0
 Identities = 11/26 (42%), Positives = 17/26 (65%)

Query: 58 LQEAKKKWIPLRKEWDVQLRFIGSLQ 83
          L+E+ + WIP+ K W +  R  G+LQ
Sbjct: 69 LEESDQLWIPVIKSWRLNERHYGALQ 94


>gnl|CDD|133084 cd06226, M14_CPT_like, Peptidase M14-like domain of an
           uncharacterized group of Peptidase M14 Carboxypeptidase
           (CP) T (CPT)-like proteins. This group belongs to the
           M14 family of metallocarboxypeptidases (MCPs). The M14
           family are zinc-binding CPs which hydrolyze single,
           C-terminal amino acids from polypeptide chains, and have
           a recognition site for the free C-terminal carboxyl
           group, which is a key determinant of specificity. CPT
           exhibits dual-substrate specificity by cleaving
           C-terminal hydrophobic amino acid residues and
           C-terminal positively charged residues. However, CPT
           does not belong to this CPT-like group.
          Length = 293

 Score = 28.1 bits (63), Expect = 2.1
 Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 1/30 (3%)

Query: 168 GNPKPHFYLLSEI-ARECKLTKLSMGMTRD 196
             PKP F+++  I ARE    +L +    D
Sbjct: 39  TGPKPVFFIMGAIHAREYTTAELVLRFAED 68


>gnl|CDD|29936 cd00408, DHDPS-like, Dihydrodipicolinate synthase family. A member
           of the class I aldolases, which use an active-site
           lysine which stablilzes a reaction intermediate via
           Schiff base formation, and have TIM beta/alpha barrel
           fold. The dihydrodipicolinate synthase family comprises
           several pyruvate-dependent class I aldolases that use
           the same catalytic step to catalyze different reactions
           in different pathways and includes such proteins as
           N-acetylneuraminate lyase, MosA protein,
           5-keto-4-deoxy-glucarate dehydratase,
           trans-o-hydroxybenzylidenepyruvate hydratase-aldolase,
           trans-2'-carboxybenzalpyruvate hydratase-aldolase, and
           2-keto-3-deoxy- gluconate aldolase. The family is also
           referred to as the N-acetylneuraminate lyase (NAL)
           family..
          Length = 281

 Score = 26.7 bits (59), Expect = 5.1
 Identities = 11/49 (22%), Positives = 23/49 (46%), Gaps = 5/49 (10%)

Query: 136 GIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKP-----HFYLLSE 179
           G+  N T++ + L R   +   +G++ +PP    P       HF  +++
Sbjct: 72  GVGANSTREAIELARHAEEAGADGVLVVPPYYNKPSQEGIVAHFKAVAD 120


>gnl|CDD|32721 COG2896, MoaA, Molybdenum cofactor biosynthesis enzyme [Coenzyme
           metabolism].
          Length = 322

 Score = 26.7 bits (59), Expect = 5.5
 Identities = 22/85 (25%), Positives = 34/85 (40%), Gaps = 12/85 (14%)

Query: 70  KEWDVQLRFI-----GSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYI 124
           KE   QLRFI     G   S ++ + +SL +++  +     A+LL +      R    Y 
Sbjct: 177 KERGAQLRFIELMPLGEGNSWRLDKYLSLDEILRKLEER--ATLLPVRKRLHGR--AKYF 232

Query: 125 QVNTGYEIQKSGIMPNQTKDFVILC 149
               G EI   G +   +  F   C
Sbjct: 233 IHPDGGEI---GFIAPVSNPFCATC 254


>gnl|CDD|153344 cd07660, BAR_Arfaptin, The Bin/Amphiphysin/Rvs (BAR) domain of
           Arfaptin.  The BAR domain of Arfaptin-like proteins,
           also called the Arfaptin domain, is a dimerization and
           lipid binding module that can detect and drive membrane
           curvature. Arfaptins are ubiquitously expressed proteins
           implicated in mediating cross-talk between Rac, a member
           of the Rho family GTPases, and Arf (ADP-ribosylation
           factor) small GTPases. Arfaptins bind to GTP-bound Arf1,
           Arf5, and Arf6, with strongest binding to GTP-Arf1.
           Arfaptins also bind to Rac-GTP and Rac-GDP with similar
           affinities. The Arfs are thought to bind to the same
           surface as Rac, and their binding is mutually exclusive.
           Mammals contain at least two isoforms of Arfaptin.
           Arfaptin 1 has been shown to inhibit the activation of
           Arf-dependent phospholipase D (PLD) and the secretion of
           matrix metalloproteinase-9 (MMP-9), an enzyme implicated
           in cancer invasiveness and metastasis. Arfaptin 2
           regulates the aggregation of the protein huntingtin,
           which is implicated in Huntington disease. Arfaptins are
           single-domain proteins with a BAR-like structure. BAR
           domains form dimers that bind to membranes, induce
           membrane bending and curvature, and may also be involved
           in protein-protein interactions.
          Length = 201

 Score = 26.5 bits (59), Expect = 6.1
 Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 3/35 (8%)

Query: 54  AENKLQEAKKKWIPLRKEWDVQLRFIGSLQSNKVS 88
           A+ + Q  K K+  LR +  V+L+F   L+ NKV 
Sbjct: 139 AQRRFQAHKDKYEKLRNDVSVKLKF---LEENKVK 170


>gnl|CDD|145200 pfam01905, DevR, CRISPR-associated negative autoregulator
           DevR/Csa2.  This group of families is one of several
           protein families that are always found associated with
           prokaryotic CRISPRs, themselves a family of clustered
           regularly interspaced short palindromic repeats, DNA
           repeats found in nearly half of all bacterial and
           archaeal genomes. These DNA repeat regions have a
           remarkably regular structure: unique sequences of
           constant size, called spacers, sit between each pair of
           repeats. It has been shown that the CRISPRs are
           virus-derived sequences acquired by the host to enable
           them to resist viral infection. The Cas proteins from
           the host use the CRISPRs to mediate an antiviral
           response. After transcription of the CRISPR, a complex
           of Cas proteins termed Cascade cleaves a CRISPR RNA
           precursor in each repeat and retains the cleavage
           products containing the virus-derived sequence. Assisted
           by the helicase Cas3, these mature CRISPR RNAs then
           serve as small guide RNAs that enable Cascade to
           interfere with virus proliferation. Cas5 contains an
           endonuclease motif, whose inactivation leads to loss of
           resistance, even in the presence of phage-derived
           spacers. This family used to be known as DUF73. DevR
           appears to be negative autoregulator within the system.
          Length = 293

 Score = 26.1 bits (58), Expect = 7.3
 Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 9/57 (15%)

Query: 73  DVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSL-----EMI--KQSRFLPV 122
           ++ L  IG   + +++    + DV E   R K A+L +L          K++RFLPV
Sbjct: 185 NLDLDRIGRPSAEQING-NYVLDVDERKRRIK-AALKALLLLLSGPFGAKRARFLPV 239


>gnl|CDD|35456 KOG0235, KOG0235, KOG0235, Phosphoglycerate mutase [Carbohydrate
           transport and metabolism].
          Length = 214

 Score = 26.1 bits (57), Expect = 8.0
 Identities = 11/37 (29%), Positives = 17/37 (45%)

Query: 58  LQEAKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLF 94
           L+E K+K +P+   W +  R  G LQ     E    +
Sbjct: 73  LEELKQKKVPVLYTWRLNERHYGDLQGLNKRETAKRY 109


  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
   0.320    0.134    0.378 

Gapped
Lambda     K      H
   0.267   0.0695    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,461,449
Number of extensions: 118539
Number of successful extensions: 284
Number of sequences better than 10.0: 1
Number of HSP's gapped: 266
Number of HSP's successfully gapped: 25
Length of query: 222
Length of database: 6,263,737
Length adjustment: 90
Effective length of query: 132
Effective length of database: 4,318,927
Effective search space: 570098364
Effective search space used: 570098364
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 (21.8 bits)
S2: 55 (25.0 bits)