RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|255764485|ref|YP_003065139.2| hypothetical protein
CLIBASIA_03065 [Candidatus Liberibacter asiaticus str. psy62]
         (243 letters)



>gnl|CDD|35020 COG5461, COG5461, Type IV pili component [Cell motility and
           secretion].
          Length = 224

 Score =  158 bits (400), Expect = 1e-39
 Identities = 79/176 (44%), Positives = 109/176 (61%), Gaps = 1/176 (0%)

Query: 67  DYRDRYPILMRKVEQIVDIPLLAGRGEIKYPIHDTIRGFLEKYKNDSASVLFLLIPSPTV 126
           DYR R+PI++R+VE  +DIP+L G   +     D +RGFL++Y + SA  L + IPS + 
Sbjct: 37  DYRTRHPIVIREVEPEIDIPILKGDSGLTASQRDRLRGFLDRYSSASADALHIQIPSGSA 96

Query: 127 SSASIRRAVKDIRKIIISSGIPVSSISERIYDADYGMDVDTIRLSYFASKPSAGKCGFWP 186
           +  +  R  K+IR+++  SG+  + I    YDA    D   IR+SY A      KCG WP
Sbjct: 97  NEVTASRMAKEIRRLLAGSGVDRARIRVVNYDASSQEDGAPIRVSYVAYTARTPKCGQWP 156

Query: 187 EDMLGNAKGNRNWTNYGCAYQNNLAAQVVNPLDLFSPRMVTPPDAEQRDKSIQRYR 242
           ED+L N + N+N+ N+GCA Q+NLAAQV NP DL  PR +TP DAE+R   I  YR
Sbjct: 157 EDLL-NTRDNKNYYNFGCATQSNLAAQVANPRDLLGPRAMTPIDAERRAIVIDTYR 211


>gnl|CDD|36138 KOG0920, KOG0920, KOG0920, ATP-dependent RNA helicase A [RNA
           processing and modification].
          Length = 924

 Score = 29.1 bits (65), Expect = 1.0
 Identities = 25/92 (27%), Positives = 41/92 (44%), Gaps = 20/92 (21%)

Query: 106 LEKYKNDSASVLFLLIPSPTVSSASIRRAV-----KDIRKIIISSGIPVSSISERIYDAD 160
           LE     + S+ F ++P  +   +  ++AV     K  RKII+++ I  +SI+  I D  
Sbjct: 433 LEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGTRKIILATNIAETSIT--IDDVV 490

Query: 161 YGMD--------VDTIR-----LSYFASKPSA 179
           Y +D         D  R     L  + SK +A
Sbjct: 491 YVIDSGLVKEKSYDPERKVSCLLLSWVSKANA 522


>gnl|CDD|36142 KOG0924, KOG0924, KOG0924, mRNA splicing factor ATP-dependent RNA
           helicase [RNA processing and modification].
          Length = 1042

 Score = 28.8 bits (64), Expect = 1.4
 Identities = 29/133 (21%), Positives = 51/133 (38%), Gaps = 28/133 (21%)

Query: 79  VEQIVDIPLLAGRGEI------KYPIHDTI----RGFLEKYKNDSASVLFLLIPS--PTV 126
           V+Q V I L    G+I      +  I  T         +     +  +  L I S  P  
Sbjct: 551 VKQAVQIHLSGPPGDILIFMTGQEDIECTCDIIKEKLEQLDSAPTTDLAVLPIYSQLPAD 610

Query: 127 SSASI-RRAVKDIRKIIISSGIPVSSIS--------------ERIYDADYGMDV-DTIRL 170
             A I ++A   +RK I+++ I  +S++               ++Y+   GMD    + +
Sbjct: 611 LQAKIFQKAEGGVRKCIVATNIAETSLTIPGIRYVIDTGYCKLKVYNPRIGMDALQIVPI 670

Query: 171 SYFASKPSAGKCG 183
           S   +   AG+ G
Sbjct: 671 SQANADQRAGRAG 683


>gnl|CDD|107316 cd06321, PBP1_ABC_sugar_binding_like_11, Periplasmic sugar-binding
           domain of uncharacterized ABC-type transport systems.
           This group includes the periplasmic sugar-binding domain
           of uncharacterized ABC-type transport systems that share
           homology with a family of pentose/hexose sugar-binding
           proteins of the type I periplasmic binding protein
           superfamily, which consist of two domains connected by a
           three-stranded hinge. The substrate specificity of this
           group is not known, but it is predicted to be involved
           in the transport of sugar-containing molecules and
           chemotaxis.
          Length = 271

 Score = 28.8 bits (65), Expect = 1.5
 Identities = 6/17 (35%), Positives = 12/17 (70%)

Query: 140 KIIISSGIPVSSISERI 156
            + I +G PVS++ +R+
Sbjct: 123 NVAILNGPPVSAVLDRV 139


>gnl|CDD|133305 cd04105, SR_beta, Signal recognition particle receptor, beta
           subunit (SR-beta).  SR-beta and SR-alpha form the
           heterodimeric signal recognition particle (SRP or SR)
           receptor that binds SRP to regulate protein
           translocation across the ER membrane.  Nascent
           polypeptide chains are synthesized with an N-terminal
           hydrophobic signal sequence that binds SRP54, a
           component of the SRP.  SRP directs targeting of the
           ribosome-nascent chain complex (RNC) to the ER membrane
           via interaction with the SR, which is localized to the
           ER membrane.  The RNC is then transferred to the
           protein-conducting channel, or translocon, which
           facilitates polypeptide translation across the ER
           membrane or integration into the ER membrane.  SR-beta
           is found only in eukaryotes; it is believed to control
           the release of the signal sequence from SRP54 upon
           binding of the ribosome to the translocon.  High
           expression of SR-beta has been observed in human colon
           cancer, suggesting it may play a role in the development
           of this type of cancer.
          Length = 203

 Score = 28.4 bits (64), Expect = 2.0
 Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 7/46 (15%)

Query: 94  IKYPIHDTIR-GFLEKYKNDSASVLFLLIPSPTVSSASIRRAVKDI 138
           +  P H  +R   LE  KN +  ++F+      V SA+ ++ +KD+
Sbjct: 53  VDVPGHPKLRDKLLETLKNSAKGIVFV------VDSATFQKNLKDV 92


>gnl|CDD|133040 cd04197, eIF-2B_epsilon_N, The N-terminal domain of epsilon subunit
           of the eIF-2B is a subfamily of glycosyltransferase 2.
           N-terminal domain of epsilon subunit of the eukaryotic
           translation initiation factor 2B (eIF-2B): eIF-2B is a
           guanine nucleotide-exchange factor which mediates the
           exchange of GDP (bound to initiation factor eIF2) for
           GTP, generating active eIF2.GTP complex. EIF2B is a
           complex multimeric protein consisting of five subunits
           named alpha, beta, gamma, delta and epsilon. Subunit
           epsilon shares sequence similarity with gamma subunit,
           and with a family of bifunctional nucleotide-binding
           enzymes such as ADP-glucose pyrophosphorylase,
           suggesting that epsilon subunit may play roles in
           nucleotide binding activity. In yeast, eIF2B gamma
           enhances the activity of eIF2B-epsilon leading to the
           idea that these subunits form the catalytic subcomplex.
          Length = 217

 Score = 27.2 bits (61), Expect = 4.0
 Identities = 13/78 (16%), Positives = 28/78 (35%), Gaps = 11/78 (14%)

Query: 118 FLLIPSPTVSSASIRRAV---KDIRK--------IIISSGIPVSSISERIYDADYGMDVD 166
           F+L+    VS+  ++  +   K+ RK        +++    P         +    +D  
Sbjct: 107 FILVSGDVVSNIDLKEILEEHKERRKKDKNAIMTMVLKEASPPHRTRRTGEEFVIAVDPK 166

Query: 167 TIRLSYFASKPSAGKCGF 184
           T RL ++   P +     
Sbjct: 167 TSRLLHYEELPGSKYRSI 184


>gnl|CDD|36140 KOG0922, KOG0922, KOG0922, DEAH-box RNA helicase [RNA processing
           and modification].
          Length = 674

 Score = 26.4 bits (58), Expect = 6.8
 Identities = 23/117 (19%), Positives = 44/117 (37%), Gaps = 26/117 (22%)

Query: 88  LAGRGEIKYPIHDTIRGFLEKY-KNDSASVLFLLIP-----SPTVSSASIRRAVKDIRKI 141
           L G+ EI     +     L +  K+       L++P          S     A    RK+
Sbjct: 265 LTGQEEI-----EAACELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGKRKV 319

Query: 142 IISSGIPVSSIS--------------ERIYDADYGMDV-DTIRLSYFASKPSAGKCG 183
           I+S+ I  +S++              ++ Y+   G+D    + +S  ++   AG+ G
Sbjct: 320 ILSTNIAETSLTIDGIRYVVDSGFVKQKKYNPRTGLDSLIVVPISKASANQRAGRAG 376


>gnl|CDD|37337 KOG2126, KOG2126, KOG2126, Glycosylphosphatidylinositol anchor
           synthesis protein [Signal transduction mechanisms].
          Length = 895

 Score = 26.4 bits (58), Expect = 7.1
 Identities = 9/25 (36%), Positives = 13/25 (52%)

Query: 24  SLISCLKTIFWKNFFLRTLMLGQLF 48
           S I+   TI     F R LM+ ++F
Sbjct: 836 STITVTSTILVVTIFRRHLMVWKIF 860


>gnl|CDD|73401 cd04739, DHOD_like, Dihydroorotate dehydrogenase (DHOD) like
           proteins.  DHOD catalyzes the oxidation of
           (S)-dihydroorotate to orotate. This is the fourth step
           and the only redox reaction in the de novo biosynthesis
           of UMP, the precursor of all pyrimidine nucleotides.
           DHOD requires FMN as co-factor. DHOD divides into class
           1 and class 2 based on their amino acid sequences and
           cellular location. Members of class 1 are cytosolic
           enzymes and multimers while class 2 enzymes are membrane
           associated and monomeric. The class 1 enzymes can be
           further divided into subtypes 1A and 1B which are
           homodimers and heterotetrameric proteins, respectively. 
           This subgroup has the conserved FMN binding site, but
           lacks some catalytic residues and may therefore be
           inactive..
          Length = 325

 Score = 26.3 bits (58), Expect = 7.7
 Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 6/45 (13%)

Query: 51  LLFYGTS---ALAYYDEGSDYR---DRYPILMRKVEQIVDIPLLA 89
            L YG+S   AL+Y+ E   Y    + Y  L+R+ ++ V IP++A
Sbjct: 60  FLTYGSSFAEALSYFPEYGRYNLGPEEYLELIRRAKRAVSIPVIA 104


>gnl|CDD|48641 cd03414, CbiX_SirB_C, Sirohydrochlorin cobalt chelatase (CbiX) and
           sirohydrochlorin iron chelatase (SirB), C-terminal
           domain. SirB catalyzes the ferro-chelation of
           sirohydrochlorin to siroheme, the prosthetic group of
           sulfite and nitrite reductases. CbiX is a
           cobaltochelatase, responsible for the chelation of Co2+
           into sirohydrochlorin, an important step in the vitamin
           B12 biosynthetic pathway. CbiX often contains a
           C-terminal histidine-rich region that may be important
           for metal delivery and/or storage, and may also contain
           an iron-sulfur center. Both CbiX and SirB are found in a
           wide range of bacteria..
          Length = 117

 Score = 26.3 bits (58), Expect = 8.4
 Identities = 15/100 (15%), Positives = 32/100 (32%), Gaps = 9/100 (9%)

Query: 87  LLAGRG----EIKYPIHDTIRGFLEKYKNDSASVLFLLIPSPTVSSASIRRAVKDIRKII 142
           +L GRG    +    +    R   E          F     P++  A  R      R+++
Sbjct: 4   VLVGRGSSDPDANADVAKIARLLEEGTGFARVETAFAAATRPSLPEALERLRALGARRVV 63

Query: 143 ISS-----GIPVSSISERIYDADYGMDVDTIRLSYFASKP 177
           +       G+ +  I E++ +      ++ +        P
Sbjct: 64  VLPYLLFTGVLMDRIEEQVAELAAEPGIEFVLAPPLGPHP 103


>gnl|CDD|34402 COG4792, EscU, Type III secretory pathway, component EscU
           [Intracellular trafficking and secretion].
          Length = 349

 Score = 26.0 bits (57), Expect = 8.9
 Identities = 9/46 (19%), Positives = 23/46 (50%), Gaps = 6/46 (13%)

Query: 16  FKGLANMRSLISCLKTIFWKNFFLRTLMLGQLFFLLLFYGTSALAY 61
            K + ++RS++  LK++       + ++L  +F+ +L    +   Y
Sbjct: 128 AKRIFSLRSVVELLKSLL------KVVVLSLIFWFMLHGYANTFLY 167


  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
   0.325    0.141    0.426 

Gapped
Lambda     K      H
   0.267   0.0785    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,078,734
Number of extensions: 166664
Number of successful extensions: 574
Number of sequences better than 10.0: 1
Number of HSP's gapped: 573
Number of HSP's successfully gapped: 23
Length of query: 243
Length of database: 6,263,737
Length adjustment: 91
Effective length of query: 152
Effective length of database: 4,297,318
Effective search space: 653192336
Effective search space used: 653192336
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 56 (25.2 bits)