RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

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



>gnl|CDD|34268 COG4649, COG4649, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 221

 Score =  121 bits (305), Expect = 1e-28
 Identities = 64/190 (33%), Positives = 100/190 (52%), Gaps = 1/190 (0%)

Query: 23  WIAPLLILMILSLAIWFYLFDGSHEKKKNIVGENFAQALELFNSNKLDDARSSFEKILSQ 82
            +  + IL++L  A +   +      + +  G+ F  AL+L   NK DDA ++F  +   
Sbjct: 29  AVIGIAILVVLGTAGY-VGYTYWQTSRASKSGDAFLAALKLAQENKTDDALAAFTDLEKT 87

Query: 83  DNKLYNPLSNMYIASILVAKGDTKNAAEIFLKVANDDLAPLAVRYAATLQAASILVDTSS 142
               Y  L+ M  A++L  KGDT  A   F ++A D   P   R  A L+AA +LVD  S
Sbjct: 88  GYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLARLRAAYLLVDNGS 147

Query: 143 YEEISKILQKLSEPSNPMHQFANEILGISALKFGKVQKAKTIFEELAKDNNSPFGISTRS 202
           Y+++S  ++ L+   NPM   A E LG++A K G   KAK+ F ++A D  +P  I  R+
Sbjct: 148 YDDVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIANDAQAPRNIRQRA 207

Query: 203 QMILANIIAS 212
           Q++L  I +S
Sbjct: 208 QIMLDLIDSS 217


>gnl|CDD|31915 COG1729, COG1729, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 262

 Score = 40.0 bits (93), Expect = 5e-04
 Identities = 27/102 (26%), Positives = 47/102 (46%), Gaps = 10/102 (9%)

Query: 57  FAQALELFNSNKLDDARSSFEKILSQ-DNKLYNPLSNMYIASILVAKGDTKNAAEIFLKV 115
           +  AL+L+ S    +A  +F+  + +  N  Y P +  ++   L A+GD ++AA IF +V
Sbjct: 145 YNAALDLYKSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARV 204

Query: 116 AND----DLAPLAVRYAATLQAASILVDTSSYEEISKILQKL 153
             D      AP      A L+    L    + +E    LQ++
Sbjct: 205 VKDYPKSPKAP-----DALLKLGVSLGRLGNTDEACATLQQV 241


>gnl|CDD|37216 KOG2005, KOG2005, KOG2005, 26S proteasome regulatory complex,
           subunit RPN1/PSMD2 [Posttranslational modification,
           protein turnover, chaperones].
          Length = 878

 Score = 34.1 bits (78), Expect = 0.033
 Identities = 30/124 (24%), Positives = 51/124 (41%), Gaps = 13/124 (10%)

Query: 84  NKLYNPLSNMYIASIL---VAKGDTKN--AAEIFLKVANDDLAPLAVRYAATLQAASILV 138
           + L +  S   I +IL   +A   ++     E+   +  D  +P+ V   A+L    I V
Sbjct: 459 DYLQSSSSIHRIGAILGLGLAYAGSQREEVLELLSPIMFDTKSPMEVVAFASLSLGMIFV 518

Query: 139 DTSSYEEISKILQKL-----SEPSNPMHQFANEILGISALKFGKVQKAKTIFEELAKDNN 193
            + + +  S ILQ L     +E  +   +F    LG++ L  GK Q++     E  K   
Sbjct: 519 GSCNEDVTSSILQTLMEKSETELEDQWFRFL--ALGLALLFLGK-QESVDAVVETIKAIE 575

Query: 194 SPFG 197
            P  
Sbjct: 576 GPIR 579


>gnl|CDD|113045 pfam04258, Peptidase_A22B, Signal peptide peptidase.  The members
           of this family are membrane proteins. In some proteins
           this region is found associated with pfam02225. This
           family corresponds with Merops subfamily A22B, the type
           example of which is signal peptide peptidase. There is a
           sequence-similarity relationship with pfam01080.
          Length = 294

 Score = 30.4 bits (69), Expect = 0.40
 Identities = 10/50 (20%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 11  KGKCKMGKCCYKWIAPLLILMILSLAI--WFYLFDGSHEKKKNIVGENFA 58
           K K K+     ++    L+ ++L +    W+Y+    H   ++I+G    
Sbjct: 80  KKKSKLELKNGRFTYSELVALLLCIVFAVWWYVLRKEHWILQDILGIALC 129


>gnl|CDD|37287 KOG2076, KOG2076, KOG2076, RNA polymerase III transcription factor
           TFIIIC [Transcription].
          Length = 895

 Score = 29.9 bits (67), Expect = 0.52
 Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 2/60 (3%)

Query: 57  FAQALELFNSNKLDDARSSFEKILSQDNKLYNPLSNMYIASILVAKGDTKNAAEIFLKVA 116
             +A  LF    L++A     +++ QD +         +  I   +GD + A   +L  A
Sbjct: 143 LGEANNLFARGDLEEAEEILMEVIKQDPRNPIAYY--TLGEIYEQRGDIEKALNFWLLAA 200


>gnl|CDD|30564 COG0215, CysS, Cysteinyl-tRNA synthetase [Translation, ribosomal
           structure and biogenesis].
          Length = 464

 Score = 28.7 bits (64), Expect = 1.3
 Identities = 23/108 (21%), Positives = 41/108 (37%), Gaps = 11/108 (10%)

Query: 64  FNSNKLDDARSSFEKILSQDNKLYNPLSNMYIASILVAKGDTKNAAEIFLKVANDDLA-P 122
           F+   L++A+ + E+       LYN L  +   +      D K     F +  +DD   P
Sbjct: 306 FSEELLEEAKKALER-------LYNALRRLRDLAGDAELADLKEFEARFREALDDDFNTP 358

Query: 123 LAVRYAATLQAASILVDTSSYEEISKILQKLSEPSNPMHQFANEILGI 170
            A+   A L   +  ++    E  S     LS     +     ++LG+
Sbjct: 359 KAL---AVLFELAKEINRLLEEGKSDAKAVLSALKALLAILGLKVLGL 403


>gnl|CDD|33593 COG3799, Mal, Methylaspartate ammonia-lyase [Amino acid transport
           and metabolism].
          Length = 410

 Score = 28.4 bits (63), Expect = 1.4
 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 6/82 (7%)

Query: 87  YNPLSNMYIASILVAKGDTK--NAAEIFLKVANDDLAPLAVRYA---ATLQAASILVDTS 141
           + P  N ++  +LV +      + A +F K+ + +L   AVRY    A L AA++   T+
Sbjct: 89  FIPFLNDHVKPLLVGRDVDAFLDNARVFEKLIDGNLLHTAVRYGVSQALLDAAALATGTT 148

Query: 142 SYEEISKILQKLSEPSNPMHQF 163
             E +    Q L   +  +  F
Sbjct: 149 KTEVVCDEWQ-LPRVTESVPLF 169


>gnl|CDD|113791 pfam05034, MAAL_N, Methylaspartate ammonia-lyase N-terminus.
           Methylaspartate ammonia-lyase EC:4.3.1.2 catalyses the
           second step of fermentation of glutamate. It is a
           homodimer. This family represents the N-terminal region
           of Methylaspartate ammonia-lyase. This domain is
           structurally related to pfam03952. This domain is
           associated with the catalytic domain pfam07476.
          Length = 158

 Score = 28.6 bits (64), Expect = 1.5
 Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 5/61 (8%)

Query: 89  PLSNMYIASILVAKGDT--KNAAEIFLKVANDDLAPLAVRYA---ATLQAASILVDTSSY 143
           P++   +A  L+ +  +   + A    K+ + +    A+RY    A L AA+    T+  
Sbjct: 90  PVTERVVAPRLIGRDVSRFLDNAAKVDKLIDGNRLHTAIRYGVSQALLDAAAHARRTTMA 149

Query: 144 E 144
           E
Sbjct: 150 E 150


>gnl|CDD|143395 cd06534, ALDH-SF, NAD(P)+-dependent aldehyde dehydrogenase
           superfamily.  The aldehyde dehydrogenase superfamily
           (ALDH-SF) of  NAD(P)+-dependent enzymes, in general,
           oxidize a wide range of  endogenous and exogenous
           aliphatic and aromatic aldehydes to their corresponding
           carboxylic acids and play an  important role in
           detoxification. Besides aldehyde detoxification, many
           ALDH isozymes possess multiple additional catalytic and
           non-catalytic functions such as participating in
           metabolic pathways, or as binding proteins, or
           osmoregulants, to mention a few. The enzyme has three
           domains, a NAD(P)+ cofactor-binding domain, a catalytic
           domain, and a bridging domain; and the active enzyme is
           generally either homodimeric or homotetrameric. The
           catalytic mechanism is proposed to involve cofactor
           binding, resulting in a conformational change and
           activation of an invariant catalytic cysteine
           nucleophile. The cysteine and aldehyde substrate form an
           oxyanion thiohemiacetal intermediate resulting in
           hydride transfer to the cofactor and formation of a
           thioacylenzyme intermediate. Hydrolysis of the
           thioacylenzyme and release of the carboxylic acid
           product occurs, and in most cases, the reduced cofactor
           dissociates from the enzyme. The evolutionary
           phylogenetic tree of ALDHs appears to have an initial
           bifurcation between what has been characterized as the
           classical aldehyde dehydrogenases, the ALDH family
           (ALDH) and extended family members or aldehyde
           dehydrogenase-like (ALDH-L) proteins. The ALDH proteins
           are represented by enzymes which share a number of
           highly conserved residues necessary for catalysis and
           cofactor binding and they include such proteins as
           retinal dehydrogenase, 10-formyltetrahydrofolate
           dehydrogenase, non-phosphorylating glyceraldehyde
           3-phosphate dehydrogenase,
           delta(1)-pyrroline-5-carboxylate dehydrogenases,
           alpha-ketoglutaric semialdehyde dehydrogenase,
           alpha-aminoadipic semialdehyde dehydrogenase, coniferyl
           aldehyde dehydrogenase and succinate-semialdehyde
           dehydrogenase.  Included in this larger group are all
           human, Arabidopsis, Tortula, fungal, protozoan, and
           Drosophila ALDHs identified in families ALDH1 through
           ALDH22 with the exception of families ALDH18, ALDH19,
           and ALDH20 which are present in the ALDH-like group. The
           ALDH-like group is represented by such proteins as
           gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA
           reductase, and coenzyme A acylating aldehyde
           dehydrogenase. All of these proteins have a conserved
           cysteine that aligns with the catalytic cysteine of the
           ALDH group.
          Length = 367

 Score = 27.2 bits (61), Expect = 3.8
 Identities = 27/105 (25%), Positives = 43/105 (40%), Gaps = 19/105 (18%)

Query: 106 KNAAEIFLKVANDDLAPLAVRYAATLQ------AAS-ILVDTSSYEEISKILQKLSEPSN 158
           K+   I  + A+ D A     + A         AAS +LV  S Y+E  + L  +    +
Sbjct: 205 KSPV-IVDEDADLDAAVEGAVFGAFFNAGQICTAASRLLVHESIYDEFVEKLVTVLVDVD 263

Query: 159 PMHQFAN-EILGISALKFGKVQ---KAKTIFEELAKDNNSPFGIS 199
           P    A  EI       FG V    + K   E +A  N++ +G++
Sbjct: 264 PDMPIAQEEI-------FGPVLPVIRFKDEEEAIALANDTEYGLT 301


>gnl|CDD|37213 KOG2002, KOG2002, KOG2002, TPR-containing nuclear phosphoprotein
           that regulates K(+) uptake [Inorganic ion transport and
           metabolism].
          Length = 1018

 Score = 26.9 bits (59), Expect = 4.2
 Identities = 20/135 (14%), Positives = 50/135 (37%), Gaps = 3/135 (2%)

Query: 60  ALELFNSNKLDDARSSFEKILSQDNKLYNPLSNMYIASILVAKGDTKNAAEIFLKVANDD 119
            L   +S+         ++   ++N   NP++  ++A+    K D +    +      + 
Sbjct: 243 DLNFNDSDSYKKGVQLLQRAYKENN--ENPVALNHLANHFYFKKDYERVWHLAEHAIKNT 300

Query: 120 LAPLAVRYAATLQAASILVDTSSYEEISKILQKLSEPSNPMHQFANEILGISALKFGKVQ 179
               +++  +  Q          +E+  K   +  +  N         LG   +K G ++
Sbjct: 301 ENK-SIKAESFYQLGRSYHAQGDFEKAFKYYMESLKADNDNFVLPLVGLGQMYIKRGDLE 359

Query: 180 KAKTIFEELAKDNNS 194
           ++K  FE++ K   +
Sbjct: 360 ESKFCFEKVLKQLPN 374


>gnl|CDD|37035 KOG1824, KOG1824, KOG1824, TATA-binding protein-interacting protein
           [General function prediction only].
          Length = 1233

 Score = 26.5 bits (58), Expect = 5.6
 Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 8/70 (11%)

Query: 126 RYAAT------LQAASILVDTSSYEEISK-ILQKLSEPSNPMHQFANEILGISALKFGKV 178
           R+ AT      LQ  SI +D  S  ++ K +L+ L + +  +   A + LG    K  + 
Sbjct: 22  RFMATSDLMTELQKDSIKLDDDSERKVVKMLLKLLEDKNGEVQNLAVKCLGPLVSKVKE- 80

Query: 179 QKAKTIFEEL 188
            + +TI E L
Sbjct: 81  DQLETIVENL 90


>gnl|CDD|37214 KOG2003, KOG2003, KOG2003, TPR repeat-containing protein [General
           function prediction only].
          Length = 840

 Score = 26.6 bits (58), Expect = 5.9
 Identities = 19/79 (24%), Positives = 30/79 (37%), Gaps = 2/79 (2%)

Query: 41  LFDGSHEKKKNIVGENFAQALELFNSNKLDDARSSFEKILSQDNKLYNPLSNMYIASILV 100
           +F+    K  +    N      L       DA+   +  L+ D   YN  +     +I  
Sbjct: 444 VFEKKDNKTASAAANNLCALRFLQGGKDFADAQQYADIALNIDR--YNAAALTNKGNIAF 501

Query: 101 AKGDTKNAAEIFLKVANDD 119
           A GD   AAE + +  N+D
Sbjct: 502 ANGDLDKAAEFYKEALNND 520


>gnl|CDD|143422 cd07104, ALDH_BenzADH-like, ALDH subfamily: NAD(P)+-dependent
           benzaldehyde dehydrogenase II, vanillin dehydrogenase,
           p-hydroxybenzaldehyde dehydrogenase and related
           proteins.  ALDH subfamily which includes the
           NAD(P)+-dependent, benzaldehyde dehydrogenase II (XylC,
           BenzADH, EC=1.2.1.28)  involved in the oxidation of
           benzyl alcohol to benzoate; p-hydroxybenzaldehyde
           dehydrogenase (PchA, HBenzADH) which catalyzes the
           oxidation of p-hydroxybenzaldehyde to p-hydroxybenzoic
           acid; vanillin dehydrogenase (Vdh, VaniDH) involved in
           the metabolism of ferulic acid as seen in Pseudomonas
           putida KT2440; and other related sequences.
          Length = 431

 Score = 26.0 bits (58), Expect = 9.3
 Identities = 15/64 (23%), Positives = 23/64 (35%), Gaps = 17/64 (26%)

Query: 153 LSEPSNPMHQFANEILGISALKFGKV---QKAKTIFEELAKDNNSPFGISTRSQMILANI 209
           LS+ +  M  F  EI       FG V          E +   N++ +G+S       A +
Sbjct: 323 LSDVTPDMPIFREEI-------FGPVAPVIPFDDDEEAVELANDTEYGLS-------AAV 368

Query: 210 IASD 213
              D
Sbjct: 369 FTRD 372


  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
   0.316    0.131    0.364 

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: 2,354,578
Number of extensions: 113820
Number of successful extensions: 457
Number of sequences better than 10.0: 1
Number of HSP's gapped: 453
Number of HSP's successfully gapped: 33
Length of query: 218
Length of database: 6,263,737
Length adjustment: 90
Effective length of query: 128
Effective length of database: 4,318,927
Effective search space: 552822656
Effective search space used: 552822656
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)