RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254780342|ref|YP_003064755.1| substrate-binding region of
ABC-type glycine betaine transport system [Candidatus Liberibacter
asiaticus str. psy62]
         (309 letters)



>gnl|CDD|132455 TIGR03414, ABC_choline_bnd, choline ABC transporter, periplasmic
           binding protein.  Partial phylogenetic profiling
           (PubMed:16930487) vs. the genome property of glycine
           betaine biosynthesis from choline consistently reveals a
           member of this ABC transporter periplasmic binding
           protein as the best match, save for the betaine
           biosynthesis enzymes themselves. Genomes often carry
           several paralogs, one encoded together with the permease
           and ATP-binding components and another encoded next to a
           choline-sulfatase gene, suggesting that different
           members of this protein family interact with shared
           components and give some flexibility in substrate. Of
           two members from Sinorhizobium meliloti 1021, one
           designated ChoX has been shown experimentally to bind
           choline (though not various related compounds such as
           betaine) and to be required for about 60 % of choline
           uptake. Members of this protein have an invariant Cys
           residue near the N-terminus and likely are lipoproteins.
          Length = 290

 Score =  390 bits (1003), Expect = e-109
 Identities = 136/283 (48%), Positives = 192/283 (67%), Gaps = 3/283 (1%)

Query: 19  ARDADSCTPVRFADTGWTDIAATTAMTSVILEEILGYKTNIKLLAVPVTFRSLKNKGIDI 78
           A +  SC  VRFAD GWTDI ATTA+ SV+LE  LGY+  + LL+VPVT+  LK+  +D+
Sbjct: 1   AAEPASCKTVRFADVGWTDITATTALASVLLEG-LGYQPKVTLLSVPVTYAGLKDGDLDV 59

Query: 79  FMGYWYPSLEKFIAPYLEEGSIKLVAENLQGAKYMLAVNDVGFALGIKSYQDIAKYKKEL 138
           F+G W P++E  I PYLE GS++++  NL+GAKY LAV       G+KS+ DIAK+K +L
Sbjct: 60  FLGNWMPAMEPDIKPYLESGSVEVLGPNLEGAKYTLAVPTYVADAGLKSFADIAKFKDKL 119

Query: 139 GAKIYGIEPGNEGNQRILDMINNNKFSLKGFRLIEASELASFSQIRRDQRNNIPAVFLSW 198
             KIYGIEPGN+GN+ I  MI+ N F L GF+L+E+SE    +Q+ R  +     VFL W
Sbjct: 120 DGKIYGIEPGNDGNRLIQKMIDKNAFGLGGFKLVESSEAGMLAQVARAVKRKEWVVFLGW 179

Query: 199 EPHPINSDLNIHYLPGGEEISG--FGEASVYTVVRSDYLDKCPNISRLLKNIKFSVALEN 256
           EPHP+N++  + YL GG++  G  +G A+VYT  R  Y  +CPN+ +LL N+ F++ +EN
Sbjct: 180 EPHPMNTNFKMTYLTGGDDYFGPNYGGATVYTNTRKGYAAECPNVGKLLTNLTFTLDMEN 239

Query: 257 EMMKLILNNKQDRQFVGRTMLRTHPDLLKNWLIGVTTFDGQDP 299
           ++M  ILN+ +D +   R  L+ +P++L  WL GVTT DG+D 
Sbjct: 240 QIMGAILNDGKDPEAAARQWLKANPEVLDPWLAGVTTVDGKDG 282


>gnl|CDD|172200 PRK13652, cbiO, cobalt transporter ATP-binding subunit;
           Provisional.
          Length = 277

 Score = 31.7 bits (72), Expect = 0.24
 Identities = 16/52 (30%), Positives = 26/52 (50%)

Query: 38  IAATTAMTSVILEEILGYKTNIKLLAVPVTFRSLKNKGIDIFMGYWYPSLEK 89
           I A   +  + L+  L  + ++ L ++P   RSL+ +GI I M Y Y   E 
Sbjct: 216 IVAYGTVEEIFLQPDLLARVHLDLPSLPKLIRSLQAQGIAIDMAYTYQEAED 267


>gnl|CDD|130383 TIGR01316, gltA, glutamate synthase (NADPH), homotetrameric.  This
           protein is homologous to the small subunit of NADPH and
           NADH forms of glutamate synthase as found in eukaryotes
           and some bacteria. This protein is found in numerous
           species having no homolog of the glutamate synthase
           large subunit. The prototype of the family, from
           Pyrococcus sp. KOD1, was shown to be active as a
           homotetramer and to require NADPH.
          Length = 449

 Score = 30.2 bits (68), Expect = 0.64
 Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 5/68 (7%)

Query: 66  VTFRSLKNKGIDIFMGYWYPSLEKFIAPYLEEGSIKLVAENLQGAKYMLAVNDVGFALGI 125
              +  K+ G  + +G    +LE+F+A +  +  I+   E        +AV   G A G+
Sbjct: 92  TVGKMFKDVGKPVSIG----ALERFVADWERQHGIETEPEKAPSTHKKVAVIGAGPA-GL 146

Query: 126 KSYQDIAK 133
               ++AK
Sbjct: 147 ACASELAK 154


>gnl|CDD|178068 PLN02449, PLN02449, ferrochelatase.
          Length = 485

 Score = 29.4 bits (66), Expect = 1.4
 Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 4/38 (10%)

Query: 70  SLKNKG----IDIFMGYWYPSLEKFIAPYLEEGSIKLV 103
           +L+ K     + + M YW+P  E+ I     +G  KLV
Sbjct: 172 ALEAKNLPAKVYVGMRYWHPFTEEAIDQIKADGITKLV 209


>gnl|CDD|181713 PRK09230, PRK09230, cytosine deaminase; Provisional.
          Length = 426

 Score = 27.4 bits (61), Expect = 5.1
 Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 10/65 (15%)

Query: 136 KELGAKIYGIEPGNEGNQRILDMINN---------NKFSLKGFRLIEASELASFSQIRRD 186
           + L  + YGIE GN  N  IL   N           ++S++  ++I  ++ A  + I  +
Sbjct: 359 RTLNLQDYGIEVGNPANLIILPAENGFDAVRRQVPVRYSIRHGKVIAETQPA-QTTIYLE 417

Query: 187 QRNNI 191
           Q   +
Sbjct: 418 QPEAV 422


>gnl|CDD|184443 PRK13992, minC, septum formation inhibitor; Provisional.
          Length = 205

 Score = 27.0 bits (60), Expect = 5.8
 Identities = 14/44 (31%), Positives = 21/44 (47%)

Query: 120 GFALGIKSYQDIAKYKKELGAKIYGIEPGNEGNQRILDMINNNK 163
           G  L IK YQ++     E+ AKI  +        +I  MI N++
Sbjct: 10  GLVLLIKDYQNLEDVLNEIDAKITQMGGFFAKGDKISLMIENHE 53


>gnl|CDD|180263 PRK05799, PRK05799, coproporphyrinogen III oxidase; Provisional.
          Length = 374

 Score = 26.9 bits (60), Expect = 6.4
 Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 7/68 (10%)

Query: 119 VGFALGIKSYQDIAKYKKELGAKIYGIEPGNEGNQRILDMINNNK------FSLKGFRLI 172
           +G   G  SY +  +Y+     + Y I+  NE N  + ++  N+       F   G R I
Sbjct: 257 IGCGAGAHSYVNGKRYENISNIEKY-IKEINENNSAVEEIHKNSIKDNMEEFMFMGLRKI 315

Query: 173 EASELASF 180
           +   +  F
Sbjct: 316 KGICIEDF 323


>gnl|CDD|128367 smart00052, EAL, Putative diguanylate phosphodiesterase.  Putative
           diguanylate phosphodiesterase, present in a variety of
           bacteria.
          Length = 241

 Score = 26.8 bits (60), Expect = 7.0
 Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 6/50 (12%)

Query: 41  TTAMTSVILEEI--LGYKTNIKLLAVPV----TFRSLKNKGIDIFMGYWY 84
           T      I++ I  L  K  ++++A  V        L++ G D   GY +
Sbjct: 184 TDPEDEAIVQSIIELAQKLGLQVVAEGVETPEQLDLLRSLGCDYGQGYLF 233


>gnl|CDD|178227 PLN02618, PLN02618, tryptophan synthase, beta chain.
          Length = 410

 Score = 27.0 bits (60), Expect = 7.1
 Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 7/50 (14%)

Query: 199 EPHPINSDLNIHYLPG-GEEIS---GFGEASVYTVVRSDYLDKCPNISRL 244
           EPH I++ L+    PG G E S     G A  Y+V   + L+    +SRL
Sbjct: 312 EPHSISAGLD---YPGVGPEHSFLKDTGRAEYYSVTDEEALEAFQRLSRL 358


>gnl|CDD|180213 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
          Length = 424

 Score = 26.8 bits (60), Expect = 7.2
 Identities = 11/49 (22%), Positives = 22/49 (44%), Gaps = 3/49 (6%)

Query: 240 NISRLLKNIKFSVALENEMMKLILNNKQDRQFVGRTMLRTHPDLLKNWL 288
            + + LK    S  +  +++KL+L +   R+      L    +LL N +
Sbjct: 165 ELYKRLKRSGLSPEIAEKLLKLLLEHMPPRERTAWRYLL---ELLANMI 210


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.321    0.138    0.405 

Gapped
Lambda     K      H
   0.267   0.0732    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,124,139
Number of extensions: 327776
Number of successful extensions: 658
Number of sequences better than 10.0: 1
Number of HSP's gapped: 656
Number of HSP's successfully gapped: 18
Length of query: 309
Length of database: 5,994,473
Length adjustment: 93
Effective length of query: 216
Effective length of database: 3,984,929
Effective search space: 860744664
Effective search space used: 860744664
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: 57 (25.7 bits)