RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780421|ref|YP_003064834.1| hypothetical protein
CLIBASIA_01530 [Candidatus Liberibacter asiaticus str. psy62]
         (218 letters)



>gnl|CDD|163072 TIGR02917, PEP_TPR_lipo, putative PEP-CTERM system TPR-repeat
           lipoprotein.  This protein family occurs in strictly
           within a subset of Gram-negative bacterial species with
           the proposed PEP-CTERM/exosortase system, analogous to
           the LPXTG/sortase system common in Gram-positive
           bacteria. This protein occurs in a species if and only
           if a transmembrane histidine kinase (TIGR02916) and a
           DNA-binding response regulator (TIGR02915) also occur.
           The present of tetratricopeptide repeats (TPR) suggests
           protein-protein interaction, possibly for the regulation
           of PEP-CTERM protein expression, since many PEP-CTERM
           proteins in these genomes are preceded by a proposed DNA
           binding site for the response regulator.
          Length = 899

 Score = 34.3 bits (79), Expect = 0.022
 Identities = 33/152 (21%), Positives = 54/152 (35%), Gaps = 15/152 (9%)

Query: 43  DGSHEKKKNIVGENFAQALELFNSNKLDDARSSFEKILSQDNKLYNPLSNMYIASI-LVA 101
           D   +K  N    ++ +AL  F     +DAR + +  L    +    L    +A      
Sbjct: 251 DALLKKAPNSPLAHYLKALVDFQKKNYEDARETLQDALKSAPEYLPAL---LLAGASEYQ 307

Query: 102 KGDTKNAAEIF---LKVANDDLAPLAVRYAATLQAASILVDTSSYEEISKILQKLSEPSN 158
            G+ + A +     LK A +     A R  A++Q     VD     E    L       +
Sbjct: 308 LGNLEQAYQYLNQILKYAPNS--HQARRLLASIQLRLGRVD-----EAIATLSPALG-LD 359

Query: 159 PMHQFANEILGISALKFGKVQKAKTIFEELAK 190
           P    A  +LG + L  G  +KA     +  +
Sbjct: 360 PDDPAALSLLGEAYLALGDFEKAAEYLAKATE 391



 Score = 26.2 bits (58), Expect = 6.0
 Identities = 36/128 (28%), Positives = 54/128 (42%), Gaps = 7/128 (5%)

Query: 63  LFNSNKLDDARSSFEKILSQDNKLYNPLSNMYIASILVAKGDTKNAAEIFLKVANDDLAP 122
                 L  AR +FEK LS +   +   +N+  A I + +G+  +A + F KV    L  
Sbjct: 475 YLGKGDLAKAREAFEKALSIEPDFFPAAANL--ARIDIQEGNPDDAIQRFEKV----LTI 528

Query: 123 LAVRYAATLQAASILVDTSSYEEISKILQKLSEPSNPMHQFANEILGISALKFGKVQKAK 182
                 A L  A + + T + EE    L+K +E  NP        L    L  G+++KA 
Sbjct: 529 DPKNLRAILALAGLYLRTGNEEEAVAWLEKAAE-LNPQEIEPALALAQYYLGKGQLKKAL 587

Query: 183 TIFEELAK 190
            I  E A 
Sbjct: 588 AILNEAAD 595


>gnl|CDD|151307 pfam10858, DUF2659, Protein of unknown function (DUF2659).  This
           bacterial family of proteins has no known function.
          Length = 220

 Score = 30.7 bits (69), Expect = 0.31
 Identities = 40/194 (20%), Positives = 86/194 (44%), Gaps = 11/194 (5%)

Query: 27  LLILMILSLAIWFYLFDGSHEKKKNI-----VGENFAQALEL-FNSNKLDDARSSFEKIL 80
           L I++I+SL     +   ++ K + I      G+ F ++++L    N  + A  + E ++
Sbjct: 25  LPIVIIISLIAITIMVINNNNKARQIANNQKNGDIFVKSVDLESTKNNSELAVQTLENLV 84

Query: 81  SQDNKLYNPLSNMYIASILVAKGDTKNAAEIFLKV-ANDDLAPLAVRYAATLQAASIL-- 137
           S  N     ++++   +I ++ G    A ++  K+  N + + +   YA     + ++  
Sbjct: 85  SNSNTKIQEIAHLEQVAIKISVGSFSEAKDLLNKIIENKEYSEITTSYARINWCSLVIDD 144

Query: 138 --VDTSSYEEISKILQKLSEPSNPMHQFANEILGISALKFGKVQKAKTIFEELAKDNNSP 195
             +D    E++ K L    + S P    A+    I  +K     KA+   E L + NNS 
Sbjct: 145 NNLDIDDKEKLIKYLNYFDDESKPFWATASIYKAIWDIKNNMDNKAEKNLEALIRSNNSS 204

Query: 196 FGISTRSQMILANI 209
             +  +++ +L N+
Sbjct: 205 DLLKDQAKALLQNL 218


>gnl|CDD|183314 PRK11788, PRK11788, tetratricopeptide repeat protein; Provisional.
          Length = 389

 Score = 30.5 bits (70), Expect = 0.33
 Identities = 14/69 (20%), Positives = 30/69 (43%), Gaps = 4/69 (5%)

Query: 59  QALELFNSNKLDDARSSFEKILSQDNKLYNPLSNMYIASILVAKGDTKNAAEIFLKVA-- 116
            A +      LD AR+  +K L+ D +     +++ +  + +A+GD   A E   +V   
Sbjct: 186 LAQQALARGDLDAARALLKKALAADPQ--CVRASILLGDLALAQGDYAAAIEALERVEEQ 243

Query: 117 NDDLAPLAV 125
           + +     +
Sbjct: 244 DPEYLSEVL 252


>gnl|CDD|162704 TIGR02102, pullulan_Gpos, pullulanase, extracellular,
           Gram-positive.  Pullulan is an unusual, industrially
           important polysaccharide in which short alpha-1,4 chains
           (maltotriose) are connected in alpha-1,6 linkages.
           Enzymes that cleave alpha-1,6 linkages in pullulan and
           release maltotriose are called pullulanases although
           pullulan itself may not be the natural substrate. In
           contrast, a glycogen debranching enzyme such GlgX,
           homologous to this family, can release glucose at
           alpha,1-6 linkages from glycogen first subjected to
           limit degradation by phosphorylase. Characterized
           members of this family include a surface-located
           pullulanase from Streptococcus pneumoniae
           (PubMed:11083842) and an extracellular bifunctional
           amylase/pullulanase with C-terminal pullulanase activity
           (PubMed:8798645).
          Length = 1111

 Score = 29.1 bits (65), Expect = 0.85
 Identities = 10/44 (22%), Positives = 21/44 (47%)

Query: 29  ILMILSLAIWFYLFDGSHEKKKNIVGENFAQALELFNSNKLDDA 72
              I SL  ++Y ++ +    K +  + +A++L  +N    DD 
Sbjct: 376 NTGIDSLTGYYYHYEITRGGDKVLALDPYAKSLAAWNDATSDDQ 419


>gnl|CDD|181222 PRK08073, flgL, flagellar hook-associated protein FlgL; Validated.
          Length = 287

 Score = 29.2 bits (65), Expect = 0.86
 Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 1/83 (1%)

Query: 59  QALELFNSNKLDDARSSFEKILSQDNKLYNPLSNMYIASILVAKGDTKNAAEIFLKVAND 118
           Q L   N   LD   +   ++    N +      +     L  + + K   ++ L VA  
Sbjct: 201 QPLLEENKKNLDIIINRTTEVGGTMNTV-ETFKTILSEQNLALQENRKEIEDVDLAVAIS 259

Query: 119 DLAPLAVRYAATLQAASILVDTS 141
           DLA +   Y ATL+A S +  TS
Sbjct: 260 DLAYINATYEATLKAVSTMSKTS 282


>gnl|CDD|163544 TIGR03832, Tyr_2_3_mutase, tyrosine 2,3-aminomutase.  Members of
           this protein family are tyrosine 2,3-aminomutase. It is
           variable from member to member as to whether the
           (R)-beta-Tyr or (S)-beta-Tyr is the preferred product
           from L-Tyr. This enzyme tends to occur in secondary
           metabolite biosynthesis systems, as in the production of
           chondramides in Chondromyces crocatus.
          Length = 507

 Score = 27.1 bits (60), Expect = 3.1
 Identities = 9/25 (36%), Positives = 16/25 (64%)

Query: 176 GKVQKAKTIFEELAKDNNSPFGIST 200
            K  K++ IFE +A+ N   +G++T
Sbjct: 29  AKAAKSRAIFEGIAEQNVPIYGVTT 53


>gnl|CDD|150939 pfam10345, Cohesin_load, Cohesin loading factor.  Cohesin_load is a
           common cohesin loading factor protein that is conserved
           in fungi. It is associated with the cohesin complex and
           is required in G1 for cohesin binding to chromosomes but
           dispensable in G2 when cohesion has been established. It
           is referred to as both Ssl3, in pombe, and Scc4, in
           S.cerevisiae. It complexes with Mis4.
          Length = 593

 Score = 27.3 bits (61), Expect = 3.5
 Identities = 29/126 (23%), Positives = 43/126 (34%), Gaps = 13/126 (10%)

Query: 56  NFAQALELFNSNKLDDARSSFEKILSQDNKLYNPLSN------MYIASI-LVAKGDTKNA 108
            F      F       A    E + S + KL+  L         Y+  +   +KGD + A
Sbjct: 359 LFYIIWCAFVLGDWAKADRLNEFLRSLNQKLFEKLLKDLQPLLHYLEGLYAQSKGDLEAA 418

Query: 109 AEIFLKVANDDLAPLAVRYAATLQAASILVDT--SSYEEISKILQKL----SEPSNPMHQ 162
              + KVA        +   A L    IL D       E++K+L +L    S   N    
Sbjct: 419 LYYYTKVAARKGTFRELYILALLNLVIILQDEVSRLQSELNKLLDQLEPLCSNSPNSNIL 478

Query: 163 FANEIL 168
             N +L
Sbjct: 479 LWNALL 484


>gnl|CDD|178056 PLN02437, PLN02437, ribonucleoside--diphosphate reductase large
           subunit.
          Length = 813

 Score = 26.6 bits (59), Expect = 5.0
 Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 3/58 (5%)

Query: 76  FEKILSQDNKLYNPLSNMYIASILVAKGDTKNAAEIFLKVANDDLAPLAVRYAATLQA 133
           F+KI ++  KL   LS  +   +LVA    K  A ++  V    L  LA   AA +  
Sbjct: 15  FDKITARLKKLSYGLSQDHCDPVLVA---QKVCAGVYKGVTTSQLDELAAETAAAMTT 69


>gnl|CDD|166843 PRK00187, PRK00187, multidrug efflux protein NorA; Provisional.
          Length = 464

 Score = 26.6 bits (59), Expect = 5.1
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 13/49 (26%)

Query: 28  LILMILSLAIWFYLFDGSHEKKKNIVGENFAQALELFNSNKLDDARSSF 76
           L + +L++A WF LFDG              Q + +     L DAR++F
Sbjct: 358 LAVSLLAVAAWFELFDG-------------TQTIAMGAIRGLKDARTTF 393


>gnl|CDD|130566 TIGR01502, B_methylAsp_ase, methylaspartate ammonia-lyase.  This
           model describes methylaspartate ammonia-lyase, also
           called beta-methylaspartase (EC 4.3.1.2). It follows
           methylaspartate mutase (composed of S and E subunits) in
           one of several possible pathways of glutamate
           fermentation.
          Length = 408

 Score = 26.8 bits (59), Expect = 5.2
 Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 4/62 (6%)

Query: 106 KNAAEIFLKVANDDLAPLAVRYA---ATLQAASILVDTSSYEEISKILQKLSEPSNPMHQ 162
           K+ AE+F K+  +     A+RY    A L AA+    T+  E I          +N +  
Sbjct: 109 KDMAEVFEKMTVNRNLHTAIRYGVSQALLDAAAKTRKTTMAEVIRDEYN-PGAETNAVPV 167

Query: 163 FA 164
           FA
Sbjct: 168 FA 169


>gnl|CDD|173391 PTZ00098, PTZ00098, phosphoethanolamine N-methyltransferase;
           Provisional.
          Length = 263

 Score = 26.5 bits (58), Expect = 5.9
 Identities = 12/24 (50%), Positives = 16/24 (66%)

Query: 9   SYKGKCKMGKCCYKWIAPLLILMI 32
           SY  K K+ + CYKW+ P  IL+I
Sbjct: 131 SYADKKKLFEKCYKWLKPNGILLI 154


>gnl|CDD|148332 pfam06667, PspB, Phage shock protein B.  This family consists of
          several bacterial phage shock protein B (PspB)
          sequences. The phage shock protein (psp) operon is
          induced in response to heat, ethanol, osmotic shock and
          infection by filamentous bacteriophages. Expression of
          the operon requires the alternative sigma factor
          sigma54 and the transcriptional activator PspF. In
          addition, PspA plays a negative regulatory role, and
          the integral-membrane proteins PspB and PspC play a
          positive one.
          Length = 75

 Score = 26.4 bits (59), Expect = 6.0
 Identities = 17/67 (25%), Positives = 28/67 (41%), Gaps = 10/67 (14%)

Query: 24 IAPLLILMILSLAIWFYLFDGSHEKKKN-----IVGENFAQALELFNS-NKLDDARSSFE 77
            PL+I M+    IW  L    H + K      +  E+     EL  +  KL +   + E
Sbjct: 7  AVPLIIFMLFVAPIWLIL----HYRSKWKVSQGLSEEDEQLLEELLETAEKLQERIQTLE 62

Query: 78 KILSQDN 84
          +IL  ++
Sbjct: 63 RILDAES 69


>gnl|CDD|182601 PRK10632, PRK10632, transcriptional regulator; Provisional.
          Length = 309

 Score = 26.3 bits (58), Expect = 6.7
 Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 6/40 (15%)

Query: 178 VQKAKTIFEELAKDNNSPFGI------STRSQMILANIIA 211
           + + + + E+L   NN+P G       ST +Q +LA + A
Sbjct: 73  LHEVQDVHEQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTA 112


>gnl|CDD|178951 PRK00260, cysS, cysteinyl-tRNA synthetase; Validated.
          Length = 463

 Score = 25.8 bits (58), Expect = 7.7
 Identities = 21/130 (16%), Positives = 47/130 (36%), Gaps = 24/130 (18%)

Query: 64  FNSNKLDDARSSFEKILSQDNKLYNPLSNMYIASI-LVAKGDTKNAAEIFLKVANDDLA- 121
           F+   L+ A+ + E++       YN L+   +         + +   E F++  +DD   
Sbjct: 304 FSEEALEQAKKALERL-------YNALAETALGEDDEALLAELEEFKERFIEAMDDDFNT 356

Query: 122 PLAVRYAATL----QAASILVDTSSYEEISKILQKLSEPSNPMHQFANEILGISALKFGK 177
           P A+   A L    +  +  ++T   E  + +   L            ++LG+   +   
Sbjct: 357 PEAL---AVLFELAREINRALETKDKEAAAALAALLRA--------LADVLGLEQDEEAL 405

Query: 178 VQKAKTIFEE 187
            + A     +
Sbjct: 406 FEAAADELLD 415


>gnl|CDD|139424 PRK13247, PRK13247, dihydrobiliverdin:ferredoxin oxidoreductase;
           Provisional.
          Length = 238

 Score = 26.1 bits (58), Expect = 7.7
 Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 2/46 (4%)

Query: 150 LQKLSEPSNPMHQFANEILGISALKFGKVQKAKTI--FEELAKDNN 193
           LQ L+  + P + +   ++GI  L FGK QK   +  F+ L +D +
Sbjct: 63  LQVLNSVAYPDYNYDLPLMGIDLLWFGKKQKLVAVLDFQPLVQDKD 108


>gnl|CDD|162509 TIGR01734, D-ala-DACP-lig, D-alanine--poly(phosphoribitol) ligase,
           subunit 1.  This model represents the enzyme (also
           called D-alanine-D-alanyl carrier protein ligase) which
           activates D-alanine as an adenylate via the reaction
           D-ala + ATP -> D-ala-AMP + PPi, and further catalyzes
           the condensation of the amino acid adenylate with the
           D-alanyl carrier protein (D-ala-ACP). The D-alanine is
           then further transferred to teichoic acid in the
           biosynthesis of lipoteichoic acid (LTA) and wall
           teichoic acid (WTA) in gram positive bacteria, both
           polysacchatides.
          Length = 502

 Score = 25.9 bits (57), Expect = 8.0
 Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 7/74 (9%)

Query: 134 ASILVDTSSYEEISKILQKLSEPSN-------PMHQFANEILGISALKFGKVQKAKTIFE 186
           A I VDTS   E  +++ + + P          +     +I+ +SAL+  +       F+
Sbjct: 76  AYIPVDTSIPSERIEMIIEAAGPELVIHTAELSIDAVGTQIITLSALEQAETSGGPVSFD 135

Query: 187 ELAKDNNSPFGIST 200
              K +++ + I T
Sbjct: 136 HAVKGDDNYYIIYT 149


>gnl|CDD|178486 PLN02898, PLN02898, HMP-P kinase/thiamin-monophosphate
           pyrophosphorylase.
          Length = 502

 Score = 25.9 bits (57), Expect = 9.3
 Identities = 14/60 (23%), Positives = 27/60 (45%), Gaps = 2/60 (3%)

Query: 89  PLSNMYIASILVAK-GDTKNAAEIFLKVANDDLAPLAVRYAATLQAASILVDTSSYEEIS 147
           P+  + +  ++V+  GD      I L    ++L PLA      ++ AS L+     E ++
Sbjct: 104 PVKALVVDPVMVSTSGDVLAGPSI-LSALREELLPLATIVTPNVKEASALLGGDPLETVA 162


>gnl|CDD|179079 PRK00630, PRK00630, nickel responsive regulator; Provisional.
          Length = 148

 Score = 25.5 bits (56), Expect = 9.8
 Identities = 8/22 (36%), Positives = 13/22 (59%)

Query: 160 MHQFANEILGISALKFGKVQKA 181
           + +   EI G+  +KF K+ KA
Sbjct: 120 IQRLQLEIGGLKGVKFAKLTKA 141


>gnl|CDD|178630 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing
           protein; Provisional.
          Length = 697

 Score = 25.6 bits (56), Expect = 9.8
 Identities = 9/37 (24%), Positives = 21/37 (56%), Gaps = 5/37 (13%)

Query: 161 HQFANEILGISAL-----KFGKVQKAKTIFEELAKDN 192
             F  +I+  +AL     K+G+++ A+ +F+ + + N
Sbjct: 354 TGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKN 390


  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
   0.316    0.131    0.364 

Gapped
Lambda     K      H
   0.267   0.0613    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,267,501
Number of extensions: 194229
Number of successful extensions: 568
Number of sequences better than 10.0: 1
Number of HSP's gapped: 566
Number of HSP's successfully gapped: 36
Length of query: 218
Length of database: 5,994,473
Length adjustment: 90
Effective length of query: 128
Effective length of database: 4,049,753
Effective search space: 518368384
Effective search space used: 518368384
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: 55 (25.2 bits)