RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780537|ref|YP_003064950.1| periplasmic solute binding
protein [Candidatus Liberibacter asiaticus str. psy62]
         (294 letters)



>gnl|CDD|29740 cd01137, PsaA, Metal binding protein PsaA.  These proteins have
           been shown to function as initial receptors in ABC
           transport of Mn2+ and as surface adhesins in some
           eubacterial species.  They belong to the TroA
           superfamily of periplasmic metal binding proteins that
           share a distinct fold and ligand binding mechanism. A
           typical TroA protein is comprised of two globular
           subdomains connected by a single helix and can bind the
           metal ion in the cleft between these domains. In
           addition, these proteins sometimes have a low complexity
           region containing a metal-binding histidine-rich motif
           (repetitive HDH sequence)..
          Length = 287

 Score =  300 bits (770), Expect = 3e-82
 Identities = 121/279 (43%), Positives = 170/279 (60%), Gaps = 1/279 (0%)

Query: 15  MSASATTQKKVVLSSFSIIGDITQNIAKDLVTVTTLVEAGNDSHSYQVTSADAIKIQNAD 74
            S +    K  V+++FSI+ DI +NIA D V VT++V  G D H Y+ T +D  K+  AD
Sbjct: 9   SSPATAASKLKVVATFSILADIARNIAGDRVNVTSIVPPGADPHEYEPTPSDIKKLSKAD 68

Query: 75  LILCNGLHLEETYMKYFTNLKKGTKIITVTDGINPIGVSEDTSVDSEPNPHAWMSLTNAM 134
           LIL NGL+LE    +   N  K   ++ V++GI+PI + E      +P+PHAWMS  NA+
Sbjct: 69  LILYNGLNLEPWLERLVKNAGKDVPVVAVSEGIDPIPLEEGHYKG-KPDPHAWMSPKNAI 127

Query: 135 IYIENIRKALTALDPSNAKKYELNAREYSEKIRNSILPLKTRIEKVDPEKRWFVTSEGCL 194
           IY++NI KAL+  DP+NA+ Y+ NA  Y  K++      K +   +  EKR  VTSEG  
Sbjct: 128 IYVKNIAKALSEADPANAETYQKNAAAYKAKLKALDEWAKAKFATIPAEKRKLVTSEGAF 187

Query: 195 VYLAEDFGFKSLYLWPINSDSERSPSMMRHAINQMRSHKIKFIFSESTNSDQPAKQVAYE 254
            Y A+ +G K  YLWPIN++ E +P  +   I Q++  K+  +F EST +D+  KQVA E
Sbjct: 188 SYFAKAYGLKEAYLWPINTEEEGTPKQVATLIEQVKKEKVPAVFVESTVNDRLMKQVAKE 247

Query: 255 TNASYGGVLYVDSLSKPDGPAPTYLDLLRFSLTKIVDTL 293
           T A  GG LY DSLS+  GPA TYLD++  +L  IV+ L
Sbjct: 248 TGAKIGGQLYTDSLSEKGGPADTYLDMMEHNLDTIVEGL 286


>gnl|CDD|31146 COG0803, LraI, ABC-type metal ion transport system, periplasmic
           component/surface adhesin [Inorganic ion transport and
           metabolism].
          Length = 303

 Score =  239 bits (611), Expect = 8e-64
 Identities = 104/294 (35%), Positives = 157/294 (53%), Gaps = 3/294 (1%)

Query: 1   MLRYFICLLFSYIPMSASATTQKKVVLSSFSIIGDITQNIAKDLVTVTTLVEAGNDSHSY 60
            L   + L       ++   + K  V+++F  I D+ +NIA D V V +LV  G D HSY
Sbjct: 10  ALLLILLLAGCGTSAASDGDSAKLKVVTTFPPIADVVKNIAGDKVDVVSLVPPGADPHSY 69

Query: 61  QVTSADAIKIQNADLILCNGLHLEETYMKYFTNL-KKGTKIITVTDGINPIGVSEDTSVD 119
           + T +D  K++ ADLI+ NGL LE    K   +  KK   +I V+DGI  + +  +   +
Sbjct: 70  EPTPSDIAKLRKADLIVYNGLGLEPWLEKLLESADKKKVLVIEVSDGIELLPLPGE-EEE 128

Query: 120 SEPNPHAWMSLTNAMIYIENIRKALTALDPSNAKKYELNAREYSEKIRNSILPLKTRIEK 179
              +PH W+   NA IY ENI  AL  LDP N + YE NA  Y +K+       K ++ K
Sbjct: 129 GVNDPHVWLDPKNAKIYAENIADALVELDPENKETYEKNAEAYLKKLNKLDEEAKAKLSK 188

Query: 180 VDPEKRWFVTSEGCLVYLAEDFGFKSLYLWPINSDSERSPSMMRHAINQMRSHKIKFIFS 239
           + P +R  VTS G   YLA D+G K + +  I+ ++E SP  +   ++ ++   IK IF 
Sbjct: 189 I-PAQRDVVTSHGAFGYLARDYGLKQVAIAGISPEAEPSPKDLAKLVDLIKKKNIKAIFV 247

Query: 240 ESTNSDQPAKQVAYETNASYGGVLYVDSLSKPDGPAPTYLDLLRFSLTKIVDTL 293
           ES  S + A+ +A ET     G+LY+DSL   D    TY+ +++ +L  IV+ L
Sbjct: 248 ESNVSSKSAETLAKETGVKILGLLYLDSLGDKDSKGDTYISMMKANLDTIVEGL 301


>gnl|CDD|144773 pfam01297, SBP_bac_9, Periplasmic solute binding protein family.
           This family includes periplasmic solute binding proteins
           such as TroA that interacts with an ATP-binding cassette
           transport system in Treponema pallidum.
          Length = 272

 Score =  209 bits (533), Expect = 9e-55
 Identities = 84/276 (30%), Positives = 135/276 (48%), Gaps = 13/276 (4%)

Query: 26  VLSSFSIIGDITQNIAKDLVTVTTLVEAGNDSHSYQVTSADAIKIQNADLILCNGLHLEE 85
           V++S   + D+ + I  D V VT+LV  G D H+Y+ T +D  K+  ADL++ NG  LE 
Sbjct: 1   VVASIPPLADLVKAIGGDKVEVTSLVPPGADPHTYEPTPSDIKKLAKADLVVYNGAGLEP 60

Query: 86  TYMKYFTNLKKGTKIITVTDGINPIGVSEDTSVD--------SEPNPHAWMSLTNAMIYI 137
              K   +L    K++ +++GI  +                    +PH W+   NA    
Sbjct: 61  WLDKLLASLANKVKVVDLSEGIELLDAPGHEHDHDEHDHDDHGHGDPHIWLDPKNAKAMA 120

Query: 138 ENIRKALTALDPSNAKKYELNAREYSEKIRNSILPLKTRIEKVDPEKRWFVTSEGCLVYL 197
           E I  AL+ LDP NA  YE NA  + +K+      +K ++  + P KR  +T      Y 
Sbjct: 121 EAIADALSELDPENAATYEKNAAAFLKKLDELDAEIKAKLAPI-PGKR-VITFHDAFGYF 178

Query: 198 AEDFGFKSLYLWPINSDSERSPSMMRHAINQMRSHKIKFIFSESTNSDQPAKQVAYETNA 257
           A+ +G + + +   + +SE SP+ +   I  ++ H +K IF E   S + A+ +A ET A
Sbjct: 179 AKAYGLEQIAILGESPESEPSPADLAELIKLIKEHNVKVIFVEPQFSPKLAETLAEETGA 238

Query: 258 SYGGVLYVDSLSKPDGPAPTYLDLLRFSLTKIVDTL 293
                LY+D L    G   TYL+L+R +L  + + L
Sbjct: 239 K-VVPLYLDPLGSEGG--DTYLELMRHNLDTLAEAL 271


>gnl|CDD|29736 cd01017, AdcA, Metal binding protein AcdA.  These proteins have
           been shown to function in the ABC uptake of Zn2+ and
           Mn2+ and in competence for genetic transformation and
           adhesion.  The AcdA proteins belong to the TroA
           superfamily of helical backbone metal receptor proteins
           that share a distinct fold and ligand binding mechanism.
            They are comprised of two globular subdomains connected
           by a long alpha helix and they bind their ligand in the
           cleft between these domains.  In addition, many of these
           proteins have a low complexity region containing metal
           binding histidine-rich motif (repetitive HDH sequence)..
          Length = 282

 Score =  151 bits (382), Expect = 2e-37
 Identities = 72/283 (25%), Positives = 137/283 (48%), Gaps = 12/283 (4%)

Query: 21  TQKKVVLSSFSIIGDITQNIAKDLVTVTTLVEAGNDSHSYQVTSADAIKIQNADLILCNG 80
           + K  V+++F  + + T+ I  D   V  ++ AG + H ++ +  D  +I +AD+ + NG
Sbjct: 1   SGKLKVVTTFYPLYEFTKAIGGDKADVKLIIPAGTEPHDFEPSPKDIARIADADVFVYNG 60

Query: 81  LHLEETYMKYFTNLK-KGTKIITVTDGINPIGVSE--------DTSVDSEPNPHAWMSLT 131
           L +E    K   +L+ K  K++  + GI  +             +    + +PH W+S  
Sbjct: 61  LGMETWAEKVLKSLQNKKLKVVEASKGIKLLKAGGAEHDHDHSHSHHHGDYDPHVWLSPV 120

Query: 132 NAMIYIENIRKALTALDPSNAKKYELNAREYSEKIRNSILPLKTRIEKVDPEKRWFVTSE 191
            A+  +ENI+ AL  LDP N + YE NA  Y++K+       + ++ K   + + FVT  
Sbjct: 121 LAIQQVENIKDALIKLDPDNKEYYEKNAAAYAKKLEALDQEYRAKLAKA--KGKTFVTQH 178

Query: 192 GCLVYLAEDFGFKSLYLWPINSDSERSPSMMRHAINQMRSHKIKFIFSESTNSDQPAKQV 251
               YLA  +G K + +  ++ + E SP  +   +  ++   +K+IF E   S + A+ +
Sbjct: 179 AAFGYLARRYGLKQIAIVGVSPEVEPSPKQLAELVEFVKKSDVKYIFFEENASSKIAETL 238

Query: 252 AYETNASYGGVLYVDSLSKPDGPAP-TYLDLLRFSLTKIVDTL 293
           A ET A    +  +++L+K +      Y  L++ +L  +   L
Sbjct: 239 AKETGAKLLVLNPLETLTKEEIDDGKDYFSLMKENLETLKRAL 281


>gnl|CDD|29735 cd01016, TroA, Metal binding protein TroA. These proteins have been
           shown to function as initial receptors in ABC transport
           of Zn2+ and possibly Fe3+ in many eubacterial species.
           The TroA proteins belong to the TroA superfamily of
           periplasmic metal binding proteins that share a distinct
           fold and ligand binding mechanism. A typical TroA
           protein is comprised of two globular subdomains
           connected by a single helix and can bind the metal ion
           in the cleft between these domains. In addition, these
           proteins sometimes have a low complexity region
           containing a metal-binding histidine-rich motif
           (repetitive HDH sequence)..
          Length = 276

 Score =  134 bits (339), Expect = 3e-32
 Identities = 71/276 (25%), Positives = 133/276 (48%), Gaps = 6/276 (2%)

Query: 23  KKVVLSSFSIIGDITQNIAKDLVTVTTLVEAGNDSHSYQVTSADAIKIQNADLILCNGLH 82
           K  V+++  +I D  +NI  D V VT L+  G D H Y+ T+ D  K+QNAD++  NGLH
Sbjct: 1   KPNVVTTTGMIADAVENIGGDHVEVTGLMGPGVDPHLYKATAGDVEKLQNADVVFYNGLH 60

Query: 83  LEETYMKYFTNLKKGTKIITVTDGINPIGVSEDTSVDSEPNPHAWMSLTNAMIYIENIRK 142
           LE       + L     +I + D ++   +  D   +   +PH W  +      ++ + +
Sbjct: 61  LEGKMSDVLSKLGSSKSVIALEDTLDRSQLILDEE-EGTYDPHIWFDVKLWKYAVKAVAE 119

Query: 143 ALTALDPSNAKKYELNAREYSEKIRNSILPLKTRIEKVDPEKRWFVTSEGCLVYLAEDFG 202
            L+   P +  +++ N+  Y E++ +     K +I ++  ++R  VT+     Y    +G
Sbjct: 120 VLSEKLPEHKDEFQANSEAYVEELDSLDAYAKKKIAEIPEQQRVLVTAHDAFGYFGRAYG 179

Query: 203 FKSLYLWPINSDSERSPSMMRHAINQMRSHKIKFIFSESTNSDQPAKQV-----AYETNA 257
           F+   L  I++DSE     +   ++ +   KIK IF ES+ + +  + +     A   + 
Sbjct: 180 FEVKGLQGISTDSEAGLRDINELVDLIVERKIKAIFVESSVNQKSIEALQDAVKARGHDV 239

Query: 258 SYGGVLYVDSLSKPDGPAPTYLDLLRFSLTKIVDTL 293
             GG LY D++ +      TY+ + + ++  IV+ L
Sbjct: 240 QIGGELYSDAMGEEGTSEGTYIGMFKHNVDTIVEAL 275


>gnl|CDD|29737 cd01018, ZntC, Metal binding protein ZntC.  These proteins are
           predicted to function as initial receptors in ABC
           transport of metal ions.  They belong to the TroA
           superfamily of helical backbone metal receptor proteins
           that share a distinct fold and ligand binding mechanism.
            They are comprised of two globular subdomains connected
           by a long alpha helix and bind their specific ligands in
           the cleft between these domains.  In addition, many of
           these proteins possess a metal-binding histidine-rich
           motif (repetitive HDH sequence)..
          Length = 266

 Score =  108 bits (271), Expect = 2e-24
 Identities = 64/244 (26%), Positives = 111/244 (45%), Gaps = 18/244 (7%)

Query: 37  TQNIAKDLVTVTTLVEAGNDSHSYQVTSADAIKIQNADLILCNGLHLEETYMKYFTNLKK 96
            + IA D V V  LV  G++ H+Y+       K+  ADL    GL  EE +++ F +   
Sbjct: 16  VEKIAGDTVDVVVLVPPGSNPHTYEPKPQQMKKLSEADLYFRIGLGFEEVWLERFRSNNP 75

Query: 97  GTKIITVTDGINPIGVS----EDTSVDSEP-----NPHAWMSLTNAMIYIENIRKALTAL 147
             +++ ++ GI  I ++                  +PH W+S  NA I  ENI +AL  L
Sbjct: 76  KMQVVNMSKGITLIPMADHHHHHHGEHEHHHHGNYDPHIWLSPANAKIMAENIYEALAEL 135

Query: 148 DPSNAKKYELNAREYSEKIRNSILPLKTRIEKVDPEKRWFVTSEGCLVYLAEDFGFKSLY 207
           DP NA  Y+ N      ++      ++T + K+   +R F+       Y A D+G   + 
Sbjct: 136 DPQNATYYQANLDALLAELDALDSEIRTILSKLK--QRAFMVYHPAWGYFARDYGLTQI- 192

Query: 208 LWPINSD-SERSPSMMRHAINQMRSHKIKFIFSESTNSDQPAKQVAYETNASYGGVLYVD 266
             PI  +  E SP+ ++  I+  +   ++ +F +   S + A+ +A E  A    V+ +D
Sbjct: 193 --PIEEEGKEPSPADLKRLIDLAKEKGVRVVFVQPQFSTKSAEAIAREIGA---KVVTID 247

Query: 267 SLSK 270
            L+ 
Sbjct: 248 PLAA 251


>gnl|CDD|29738 cd01019, ZnuA, Zinc binding protein ZnuA. These proteins have been
           shown to function as initial receptors in the ABC uptake
           of Zn2+.  They belong to the TroA superfamily of
           periplasmic metal binding proteins that share a distinct
           fold and ligand binding mechanism.  They are comprised
           of two globular subdomains connected by a single helix
           and bind their specific ligands in the cleft between
           these domains.  A typical TroA protein is comprised of
           two globular subdomains connected by a single helix and
           can bind the metal ion in the cleft between these
           domains. In addition, these proteins sometimes have a
           low complexity region containing a metal-binding
           histidine-rich motif (repetitive HDH sequence)..
          Length = 286

 Score =  106 bits (266), Expect = 7e-24
 Identities = 62/279 (22%), Positives = 113/279 (40%), Gaps = 29/279 (10%)

Query: 26  VLSSFSIIGDITQNIAKDLVTVTTLVEAGNDSHSYQVTSADAIKIQNADLILCNGLHLEE 85
           VL+S   +G I   I   +  V  LV  G   H Y++  +DA K+Q ADL++  G  LE 
Sbjct: 6   VLTSIKPLGFIAAAIMGGVGEVEVLVPPGASPHDYELRPSDARKLQEADLVVWIGPDLEA 65

Query: 86  TYMKYFTNLKKGTKIITVTDGINPIGVSEDTSVDSEP------------------NPHAW 127
            ++      +K  K++T+   I+   + +  S                       +PH W
Sbjct: 66  -FLDKVLQGRKKGKVLTLAKLIDLKTLEDGASHGDHEHDHEHAHGEHDGHEEGGLDPHLW 124

Query: 128 MSLTNAMIYIENIRKALTALDPSNAKKYELNAREYSEKIRNSILPLKTRI-EKVDP-EKR 185
           +S  NA    + + + L+ALDP NA  Y  N   ++ +    +  L   I E++ P + +
Sbjct: 125 LSPENAAEVAQAVAEKLSALDPDNAATYAANLEAFNAR----LAELDATIKERLAPVKTK 180

Query: 186 WFVTSEGCLVYLAEDFGFKSLYLWPINSDSERSPSMMRHAINQMRSHKIKFIFSESTNSD 245
            F        Y  + +G     ++ I+ + +     +     +++      +F+E     
Sbjct: 181 PFFVFHDAYGYFEKRYGLTQAGVFTIDPEIDPGAKRLAKIRKEIKEKGATCVFAEPQFHP 240

Query: 246 QPAKQVAYETNASYGGVLYVDSLSKPDGPAPT-YLDLLR 283
           + A+ +A  T A  G    +D L          Y++ LR
Sbjct: 241 KIAETLAEGTGAKVG---ELDPLGGLIELGKNSYVNFLR 276


>gnl|CDD|29739 cd01020, TroA_b, Metal binding protein TroA_b.  These proteins are
           predicted to function as initial receptors in ABC
           transport of metal ions.  They belong to the TroA
           superfamily of helical backbone metal receptor proteins
           that share a distinct fold and ligand binding mechanism.
            A typical TroA protein is comprised of two globular
           subdomains connected by a single helix and can bind the
           metal ion in the cleft between these domains. In
           addition, these proteins sometimes have a low complexity
           region containing a metal-binding histidine-rich motif
           (repetitive HDH sequence)..
          Length = 264

 Score = 87.3 bits (216), Expect = 4e-18
 Identities = 56/238 (23%), Positives = 98/238 (41%), Gaps = 22/238 (9%)

Query: 22  QKKVVLSSFSIIGDITQNIAKDLVTVTTLVEAGN-DSHSYQVTSADAIKIQNADLILCNG 80
            K  V++S +  G + + +  D V VT+++   + D H ++ T  DA K+  AD+++ NG
Sbjct: 1   GKINVVASTNFWGSVAEAVGGDHVEVTSIITNPDVDPHDFEPTPTDAAKVSTADIVVYNG 60

Query: 81  LHLEETYMKYFTNLKKGTKIITVTDGINPIGVSEDTSVDSEP-NPHAWMSLTNAMIYIEN 139
                 Y  + T L   TK + V      I    D   D E  NPH W            
Sbjct: 61  G----GYDPWMTKLLADTKDVIV------IAADLDGHDDKEGDNPHLWYDPETMSKVANA 110

Query: 140 IRKALTALDPSNAKKYELNAREYSEKIRNSILPLKTRIEKV--DPEKRWFVTSEGCLVYL 197
           +  AL   DP N K Y+ NA+++   ++    PL  +I ++    +      +E    YL
Sbjct: 111 LADALVKADPDNKKYYQANAKKFVASLK----PLAAKIAELSAKYKGAPVAATEPVFDYL 166

Query: 198 AEDFGFK----SLYLWPINSDSERSPSMMRHAINQMRSHKIKFIFSESTNSDQPAKQV 251
            +  G K      Y     S++E SP+ +    N +++ +I  +      +      +
Sbjct: 167 LDALGMKERTPKGYTATTESETEPSPADIAAFQNAIKNRQIDALIVNPQQASSATTNI 224


>gnl|CDD|29748 cd01145, TroA_c, Periplasmic binding protein TroA_c.  These
           proteins are predicted to function as initial receptors
           in the ABC metal ion uptake in eubacteria and archaea.
           They belong to the TroA superfamily of helical backbone
           metal receptor proteins that share a distinct fold and
           ligand binding mechanism.  A typical TroA protein is
           comprised of two globular subdomains connected by a
           single helix and can bind their ligands in the cleft
           between these domains..
          Length = 203

 Score = 81.6 bits (201), Expect = 2e-16
 Identities = 44/160 (27%), Positives = 70/160 (43%), Gaps = 6/160 (3%)

Query: 23  KKVVLSSFSIIGDITQNIAKDLVTVTTLVEAGNDSHSYQVTSADAIKIQNADLILCNGLH 82
              V+ +F  + D+ + +A D V V+ L   G D H YQ+  +D  K++ ADL++ +G  
Sbjct: 2   ALNVVVTFPDLKDLVREVAGDAVIVSALTPPGVDPHQYQLKPSDIAKMRKADLVVTSGHE 61

Query: 83  LEETYMKYFTNLKK-----GTKIITVTDGINPIGVSEDTSVDSEPNPHAWMSLTNAMIYI 137
           LE    K            G KI+        +          + NPH W+   NA    
Sbjct: 62  LEGFEPKLAELSSNSKVQPGIKILIEDSDTVGMVDRAMGDYHGKGNPHVWLDPNNAPALA 121

Query: 138 ENIRKALTALDPSNAKKYELNAREYSEKIRNSILPLKTRI 177
           + +  AL  LDPS  ++Y+ N R +  K+ N +L    R 
Sbjct: 122 KALADALIELDPSEQEEYKENLRVFLAKL-NKLLREWERQ 160


>gnl|CDD|34180 COG4531, ZnuA, ABC-type Zn2+ transport system, periplasmic
           component/surface adhesin [Inorganic ion transport and
           metabolism].
          Length = 318

 Score = 77.7 bits (191), Expect = 4e-15
 Identities = 69/296 (23%), Positives = 115/296 (38%), Gaps = 48/296 (16%)

Query: 1   MLRYFICLL--FSYIPMSASATTQKKVVLSSFSIIGDITQNIAKDLVTVTTLVEAGNDSH 58
           ML     LL     + + ++       V++S   +G I   IA  +     L+  G   H
Sbjct: 2   MLHKKTLLLSALFALLLGSAPAAAAAAVVTSIKPLGFIASAIADGVGEPEVLLPGGASPH 61

Query: 59  SYQVTSADAIKIQNADLILCNGLHLEETYMKYFTNLKKGTKIITVTD--GINPIGVSEDT 116
            Y +  +D  ++Q+ADL++  G  LE    K  + L  G K++T+ D  G+ P+   E  
Sbjct: 62  DYSLRPSDVKRLQSADLVVWVGPDLEAFLDKPLSGLP-GAKVVTLADLPGVKPLLFREAH 120

Query: 117 SVDSEP-----------------------NPHAWMSLTNAMIYIENIRKALTALDPSNAK 153
             + E                        + H W+S   A      I K L  LDP NA 
Sbjct: 121 DHEEEHDHGHDHAGADHKGDHDHHHEGEYDMHLWLSPAIAKAVAAAIAKKLAELDPQNAA 180

Query: 154 KYELNAREY-------SEKIRNSILPLKTRIEKVDPEKRWFVTSEGCLVYLAEDFGFKSL 206
           KY+ N +++        +K+   + P+K         K +FV  +    Y    +G K L
Sbjct: 181 KYDANLKDFEAQLAALDKKVGEELAPVK--------GKPFFVFHDA-YGYFENAYGLKPL 231

Query: 207 YLWPINSDSERSPSMMR-HAIN-QMRSHKIKFIFSESTNSDQPAKQVAYETNASYG 260
             + ++   E  P   R   I  Q++  K   +F+E     +  + VA  T+   G
Sbjct: 232 GHFTVS--PEVQPGAKRLAEIRTQLKEQKATCVFAEPQFRPKVVETVAEGTSVRSG 285


>gnl|CDD|29734 cd00636, TroA-like, Helical backbone metal receptor (TroA-like
           domain). These proteins have been shown to function in
           the ABC transport of ferric siderophores and metal ions
           such as Mn2+, Fe3+, Cu2+ and/or Zn2+.  Their ligand
           binding site is formed in the interface between two
           globular domains linked by a single helix.  Many of
           these proteins also possess a low complexity region
           containing a metal-binding histidine-rich motif
           (repetitive HDH sequence).  The TroA-like proteins
           differ in their fold and ligand-binding mechanism from
           the PBPI and PBPII proteins, but are structurally
           similar, however, to the beta-subunit of the nitrogenase
           molybdenum-iron protein MoFe.   Most TroA-like proteins
           are encoded by ABC-type operons and appear to function
           as periplasmic components of ABC transporters in metal
           ion uptake..
          Length = 148

 Score = 42.2 bits (98), Expect = 2e-04
 Identities = 34/180 (18%), Positives = 56/180 (31%), Gaps = 45/180 (25%)

Query: 24  KVVLSSFSIIGDITQNIAKDLVTVTTLVEAGNDS-------------HSYQVTSADAIKI 70
           K V++      ++   +  D   V     +G                H Y+  + + I  
Sbjct: 1   KRVVALDPGATELLLALGGDDKPVGVADPSGYPPEAKALLEKVPDVGHGYEP-NLEKIAA 59

Query: 71  QNADLILCNGLHLEETYMKYFTNLKKGTKIITVTDGINPIGVSEDTSVDSEPNPHAWMSL 130
              DLI+ NG  LE    K     K    ++ V +                      +SL
Sbjct: 60  LKPDLIIANGSGLEAWLDKL---SKIAIPVVVVDEASE-------------------LSL 97

Query: 131 TNAMIYIENIRKALTALDPSNAKKYELNAREYSEKIRNSILPLKTRIEKVDPEKRWFVTS 190
            N    I  I KAL           E NA E   ++   +  L+ ++ K+  +K   V  
Sbjct: 98  ENIKESIRLIGKALG---------KEENAEELIAELDARLAELRAKLAKIPKKKVSLVVG 148


>gnl|CDD|32005 COG1820, NagA, N-acetylglucosamine-6-phosphate deacetylase
           [Carbohydrate transport and metabolism].
          Length = 380

 Score = 30.6 bits (69), Expect = 0.57
 Identities = 11/41 (26%), Positives = 21/41 (51%)

Query: 76  ILCNGLHLEETYMKYFTNLKKGTKIITVTDGINPIGVSEDT 116
           I+ +G+H+    ++     K G KI+ VTD +   G+ +  
Sbjct: 243 IIADGVHVHPAAIRLALKAKGGDKIVLVTDAMAAAGLPDGE 283


>gnl|CDD|32830 COG3013, COG3013, Uncharacterized conserved protein [Function
           unknown].
          Length = 168

 Score = 29.5 bits (66), Expect = 1.1
 Identities = 14/31 (45%), Positives = 20/31 (64%), Gaps = 1/31 (3%)

Query: 127 WMSLTNAM-IYIENIRKALTALDPSNAKKYE 156
           WM +TNA  + + N  K +T LDP NA++Y 
Sbjct: 4   WMEMTNAQRLILSNQYKMMTMLDPENAERYR 34


>gnl|CDD|36399 KOG1185, KOG1185, KOG1185, Thiamine pyrophosphate-requiring enzyme
           [Amino acid transport and metabolism, Coenzyme transport
           and metabolism].
          Length = 571

 Score = 28.7 bits (64), Expect = 1.9
 Identities = 29/155 (18%), Positives = 58/155 (37%), Gaps = 28/155 (18%)

Query: 56  DSHSYQVTSADAIKIQNADLILCNGLHLEETYMKYF---TNLKKGTKIITVTDGINPIGV 112
           D+H   V+SA ++ ++ AD++L  G  L   ++ +F       K  K I V        +
Sbjct: 260 DNHPLNVSSARSLALKKADVVLLAGARLN--WILHFGLPPKWSKDVKFIQVD-------I 310

Query: 113 SEDTSVDSEPNPHAWMSLTNAMIYIENIRKALTA----LDPSN------AKKYELNAREY 162
           + +   ++   P   +   +  +++  + + L        PS        +K + N    
Sbjct: 311 NPEELGNNFVKPDVAI-QGDIGLFVLQLVEELQDQPWTWGPSTDWVKELREKDKQNEAAV 369

Query: 163 SEKIRNSILPLK-----TRIEKVDPEKRWFVTSEG 192
            EK      PL        + ++ P     + SEG
Sbjct: 370 EEKAAKKSTPLNYYQVLQTVRELLPNDDTILVSEG 404


>gnl|CDD|176330 cd01254, PH_PLD, Phospholipase D (PLD) pleckstrin homology (PH)
           domain.  Phospholipase D (PLD) pleckstrin homology (PH)
           domain.  PLD hydrolyzes phosphatidylcholine to
           phosphatidic acid (PtdOH), which can bind target
           proteins. PLD contains a PH domain, a PX domain and four
           conserved PLD signature domains. The PLD PH domain is
           specific for bisphosphorylated inositides. PH domains
           share little sequence conservation, but all have a
           common fold, which is electrostatically polarized. PH
           domains also have diverse functions. They are often
           involved in targeting proteins to the plasma membrane,
           but few display strong specificity in lipid binding.
           Any specificity is usually determined by loop regions or
           insertions in the N-terminus of the domain, which are
           not conserved across all PH domains.
          Length = 121

 Score = 28.2 bits (63), Expect = 2.4
 Identities = 7/21 (33%), Positives = 11/21 (52%)

Query: 184 KRWFVTSEGCLVYLAEDFGFK 204
           KRWF+  E  L Y+ +    +
Sbjct: 35  KRWFIVKESFLAYMDDPSSAQ 55


>gnl|CDD|30034 cd00854, NagA, N-acetylglucosamine-6-phosphate deacetylase, NagA,
           catalyzes the hydrolysis of the N-acetyl group of
           N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to
           glucosamine 6-phosphate and acetate. This is the first
           committed step in the biosynthetic pathway to
           amino-sugar-nucleotides, which is needed for cell wall
           peptidoglycan and teichoic acid biosynthesis.
           Deacetylation of N-acetylglucosamine is also important
           in lipopolysaccharide synthesis and cell wall
           recycling..
          Length = 374

 Score = 27.9 bits (62), Expect = 3.2
 Identities = 9/39 (23%), Positives = 20/39 (51%)

Query: 76  ILCNGLHLEETYMKYFTNLKKGTKIITVTDGINPIGVSE 114
           ++ +G+H+    ++     K   KI+ VTD +   G+ +
Sbjct: 242 LIADGIHVHPAAVRLAYRAKGADKIVLVTDAMAAAGLPD 280


>gnl|CDD|146493 pfam03887, YfbU, YfbU domain.  This presumed domain is about 160
           residues long. It is found in archaebacteria and
           eubacteria. In In Corynebacterium glutamicum Ycg4L it is
           associated with a helix-turn-helix domain. This suggests
           that this may be a ligand binding domain.
          Length = 166

 Score = 27.9 bits (62), Expect = 3.9
 Identities = 16/30 (53%), Positives = 18/30 (60%), Gaps = 1/30 (3%)

Query: 128 MSLTNAMIYI-ENIRKALTALDPSNAKKYE 156
           M +TNA   I  N  K + ALDP NAKKY 
Sbjct: 1   MEMTNAQRLILSNQYKLMLALDPYNAKKYR 30


>gnl|CDD|31484 COG1293, COG1293, Predicted RNA-binding protein homologous to
           eukaryotic snRNP [Transcription].
          Length = 564

 Score = 27.6 bits (61), Expect = 4.2
 Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 5/67 (7%)

Query: 137 IENIRKALTALDPSNAKKYELNAREYSEKIRNSILP-LKTRIEKVD--PEKRWFVTSEGC 193
           I     A TAL+ +  KK     RE  E I   +L   K + +K +   + RWFV+S+G 
Sbjct: 393 IAYYESAKTALEKAEGKKAIEEIRE--ELIEEGLLKSKKKKRKKKEWFEKFRWFVSSDGF 450

Query: 194 LVYLAED 200
           LV    +
Sbjct: 451 LVIGGRN 457


>gnl|CDD|176328 cd01252, PH_cytohesin, Cytohesin Pleckstrin homology (PH) domain.
           Cytohesin Pleckstrin homology (PH) domain. Cytohesin is
           an ARF-Guanine nucleotide Exchange Factor (GEF), which
           has a Sec7-type Arf-GEFdomain and a pleckstrin homology
           domain. It specifically binds
           phosphatidylinositol-3,4,5-trisphosphate (PtdIns(3,4,
           5)P3) via its PH domain and it acts as a PI 3-kinase
           effector mediating biological responses such as cell
           adhesion and membrane trafficking.  PH domains are only
           found in eukaryotes. They share little sequence
           conservation, but all have a common fold, which is
           electrostatically polarized. PH domains also have
           diverse functions. They are often involved in targeting
           proteins to the plasma membrane, but few display strong
           specificity in lipid binding.  Any specificity is
           usually determined by loop regions or insertions in the
           N-terminus of the domain, which are not conserved across
           all PH domains.
          Length = 125

 Score = 26.7 bits (59), Expect = 7.6
 Identities = 6/14 (42%), Positives = 11/14 (78%)

Query: 183 EKRWFVTSEGCLVY 196
           ++RWF+ ++ CL Y
Sbjct: 17  KRRWFILTDNCLYY 30


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

 Score = 26.8 bits (59), Expect = 8.5
 Identities = 14/43 (32%), Positives = 26/43 (60%), Gaps = 5/43 (11%)

Query: 137 IENIRKALTALDPSNAKKYELNAREYSEKIRNSILPLKTRIEK 179
            E +++ LT+L     +K EL ARE  E++++ +  +K  +EK
Sbjct: 398 QEKVQEHLTSL-----RKDELEARENLERLKSKLHEIKRYMEK 435


  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    0.132    0.377 

Gapped
Lambda     K      H
   0.267   0.0631    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,349,616
Number of extensions: 166804
Number of successful extensions: 444
Number of sequences better than 10.0: 1
Number of HSP's gapped: 425
Number of HSP's successfully gapped: 22
Length of query: 294
Length of database: 6,263,737
Length adjustment: 93
Effective length of query: 201
Effective length of database: 4,254,100
Effective search space: 855074100
Effective search space used: 855074100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (25.9 bits)