RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781203|ref|YP_003065616.1| hypothetical protein
CLIBASIA_05550 [Candidatus Liberibacter asiaticus str. psy62]
         (478 letters)



>gnl|CDD|38804 KOG3598, KOG3598, KOG3598, Thyroid hormone receptor-associated
            protein complex, subunit TRAP230 [Transcription].
          Length = 2220

 Score = 36.6 bits (84), Expect = 0.013
 Identities = 33/185 (17%), Positives = 55/185 (29%), Gaps = 34/185 (18%)

Query: 262  KHGVKSSSPGLHTSFDAYEAHTDTLAHGVDSLVRGEYPHFDQEKLQTIADNTLEDPHFKP 321
            K+G++ S+    + +D +E        G   L    +  F   ++     N  E      
Sbjct: 1710 KNGLQVSTKQKKSPWDLFE--------GTKHLAPLSWKWFGTVRVDRRVKNVEEQLRLLL 1761

Query: 322  H----LPEP-----EPLPQYKEHSDRQKPSEPLAEHPHPKRKEV-----------ERELS 361
            +    LP P      PLP   E  +  K +E   E    + +             E +  
Sbjct: 1762 YHTHVLPFPRDYYLAPLPLPPEDEEEAKKAEEEKEAAEKEEESKNAEDEKNKNTAENKKD 1821

Query: 362  EIEGAKKESSARKFFDEG------SPDHSPFKGERNQKLDPMRGADFTDAPHAKFDATTF 415
              EG K +S  ++   E       SP       +          A   +AP       T 
Sbjct: 1822 TKEGEKGKSKDKEKEGEKEKCKRASPKDDVTSEKNEHHPRASDAAAALNAPETNKGMDTQ 1881

Query: 416  TESLP 420
             + L 
Sbjct: 1882 NQKLA 1886


>gnl|CDD|34463 COG4854, COG4854, Predicted membrane protein [Function unknown].
          Length = 126

 Score = 34.9 bits (80), Expect = 0.054
 Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 4/46 (8%)

Query: 93  GAALAGKLLSFIPTPLTRLAGLALQSAPLAA----GALYAYLSHKA 134
            AAL G +L  +  PL   A  AL+ A  A      A Y Y S +A
Sbjct: 79  SAALGGAVLLALKNPLHTNAAFALEFAVCAVIVLYLAFYMYYSRRA 124


>gnl|CDD|32452 COG2271, UhpC, Sugar phosphate permease [Carbohydrate transport and
           metabolism].
          Length = 448

 Score = 32.9 bits (75), Expect = 0.18
 Identities = 18/70 (25%), Positives = 22/70 (31%), Gaps = 4/70 (5%)

Query: 74  VGTGAHLVEGLTSLAPYIAGAALAGKLLSFIPTPLTRLAGLALQSAPLAAGALYAYLSHK 133
            GT      G   L  Y+ GAALAG  L +I        G  + S       L       
Sbjct: 380 AGTAT----GFVGLFAYLIGAALAGLPLGYIADTWGWDGGFIVLSIAALLAILLLLPVWN 435

Query: 134 AESSIHHQIE 143
           AE       +
Sbjct: 436 AEERKIRDEK 445


>gnl|CDD|31074 COG0730, COG0730, Predicted permeases [General function prediction
           only].
          Length = 258

 Score = 30.4 bits (68), Expect = 1.2
 Identities = 21/94 (22%), Positives = 26/94 (27%), Gaps = 4/94 (4%)

Query: 77  GAHLVEGLTSLAPYIAGAALAGKLLSFIPTPLTRLAGLALQSAPLAAGALYAYLSHKAES 136
                  L  L   + GA L   L   +P  L +L    L    L   ALY  L  +   
Sbjct: 70  NVDWKLALILLLGALIGAFLGALLALLLPAELLKLLFGLL----LLLLALYMLLGPRLAK 125

Query: 137 SIHHQIEGVDKETADALAWREAIVHTSALLAPGA 170
           +            A AL         S L   G 
Sbjct: 126 AEDRAARLRPLLFALALLIGFLAGFLSGLFGVGG 159


>gnl|CDD|37262 KOG2051, KOG2051, KOG2051, Nonsense-mediated mRNA decay 2 protein
           [RNA processing and modification].
          Length = 1128

 Score = 29.6 bits (66), Expect = 2.1
 Identities = 29/154 (18%), Positives = 58/154 (37%), Gaps = 16/154 (10%)

Query: 327 EPLPQYKEHSDRQKPSEPLAEHPHPKRKEVERELSEIEGAKKESSARKFFDEGSPDHSPF 386
           E +P+ +E SD   P E  ++        +E   S+ +        R F++    D   F
Sbjct: 286 ELMPELEEESDEADPGEEASQMGKNGSLSIEDLWSDED-------TRAFYENL-IDLRDF 337

Query: 387 KGERNQKLDPMRGAD---FTDAPHAKFDA--TTFTESLPH-VDEQTMHRFSELKERHPVE 440
               N+  +  +  +    ++A     D   TT   S  + ++        +LKE    +
Sbjct: 338 VPATNEGFNKSKEVEKESNSEAAMVWDDREQTTEVSSPSNFMEGSIAEMKEDLKESKGED 397

Query: 441 AREVL--EGLQEKLQGTKEIKTKSLIKEAINCFL 472
            +E L     ++ L  ++     S +   ++CFL
Sbjct: 398 EKEELGKNKQEQDLLESEGDLNTSQVVSNVDCFL 431


>gnl|CDD|31004 COG0659, SUL1, Sulfate permease and related transporters (MFS
           superfamily) [Inorganic ion transport and metabolism].
          Length = 554

 Score = 29.1 bits (65), Expect = 2.5
 Identities = 35/160 (21%), Positives = 57/160 (35%), Gaps = 18/160 (11%)

Query: 90  YIAGAALAGKLLSFIPTPLTR--LAGLAL-----QSAPLAAGALYAYLSHKAESSIHHQI 142
            + G    G+L+ FIP P+     AG+A+     Q   L   A          S++   +
Sbjct: 112 ILLGLLRLGRLIRFIPRPVLIGFTAGIAILIILTQLPVLLGLASKVSGFWAKVSALFTVL 171

Query: 143 EGVDKETADALAWREAIVHTSALLAPGAIASQSIAKTVASGAVLNVPFGMVERGWSSKVL 202
             ++  T        AI+     L P  I S  IA  + +  V   P   +  G     L
Sbjct: 172 LTINLATLLLGLLTLAILLFLPRLTP-RIPSPLIALVLGTLIVWIFPLDSLRYGEIPGSL 230

Query: 203 EDHGYPDMAQHYRIFD-----MESLITDGLIGAFFGGMHS 237
                P    H+R+ +     + +L+   L  A  G + S
Sbjct: 231 -----PSGLPHFRLPNVSLSLLLALLPYALALALLGLLES 265


>gnl|CDD|34016 COG4294, Uve, UV damage repair endonuclease [DNA replication,
           recombination, and repair].
          Length = 347

 Score = 28.8 bits (64), Expect = 3.3
 Identities = 32/152 (21%), Positives = 54/152 (35%), Gaps = 18/152 (11%)

Query: 199 SKVLEDHGYPDMAQHYRIFDMESLITDGLIGAFFGGMHSKQVQNMS--LRLVNDLKEGIT 256
            + + D    D+A HYRI D   L    +     GG H  + + +   ++ +  L + + 
Sbjct: 146 REEVVDSSIRDLAYHYRILDGMGLAERSVWNLHLGGTHGGKKERLEQFIKNIQRLPDSVK 205

Query: 257 ERLPYKHGVKSSSP--------GLHTSFDAYEAHTDTLAHGVDSLVRGEYPHFDQEKLQT 308
            RL  ++  KS S          L+     ++AH   +  G+D             +L  
Sbjct: 206 SRLTLENDDKSYSTEELLPLCEKLNIPL-VFDAHHHNVHPGLDR-----EDSPSLMELIP 259

Query: 309 IADNTLEDPHFKP--HLPEPEPLPQYKEHSDR 338
               T   P  +   HL  P      + HSD 
Sbjct: 260 RIRETWTRPGLQQKVHLSSPASGTADRRHSDY 291


>gnl|CDD|39109 KOG3906, KOG3906, KOG3906, Tryptophan 2,3-dioxygenase [Amino acid
           transport and metabolism].
          Length = 399

 Score = 28.9 bits (64), Expect = 3.3
 Identities = 12/70 (17%), Positives = 24/70 (34%), Gaps = 2/70 (2%)

Query: 331 QYKEHSDRQKPSEPLAEHPHPKRKEVERELSEIEGAKKESSARKFFDEGSPDHSPFKGER 390
           +Y++  +R               +E  ++L+E    K     +  FD    +     G R
Sbjct: 220 KYEKSVNRYLEDLAKQAADPSNTEEKAKQLAEYH--KTAEVFQSIFDPRQHEQLIRNGNR 277

Query: 391 NQKLDPMRGA 400
                 ++GA
Sbjct: 278 RLSHRALQGA 287


>gnl|CDD|177083 CHL00181, cbbX, CbbX; Provisional.
          Length = 287

 Score = 28.5 bits (64), Expect = 4.7
 Identities = 11/22 (50%), Positives = 15/22 (68%)

Query: 255 ITERLPYKHGVKSSSPGLHTSF 276
           + +RL    G+ SS+PGLH SF
Sbjct: 43  LIDRLRKNLGLTSSNPGLHMSF 64


>gnl|CDD|37349 KOG2138, KOG2138, KOG2138, Predicted RNA binding protein, contains
           G-patch domain [RNA processing and modification].
          Length = 883

 Score = 28.1 bits (62), Expect = 5.1
 Identities = 16/77 (20%), Positives = 33/77 (42%)

Query: 317 PHFKPHLPEPEPLPQYKEHSDRQKPSEPLAEHPHPKRKEVERELSEIEGAKKESSARKFF 376
           P FKP+  E   +P  ++H  ++   +   E      K  + +  + +G +K    +K  
Sbjct: 788 PVFKPNASETLEVPLKEKHKKKKDKHKKKKEKRRKSEKSKKHKKHKKKGKQKNRKPKKSS 847

Query: 377 DEGSPDHSPFKGERNQK 393
              S D S  + ++ +K
Sbjct: 848 SSESSDSSDKQSDKEKK 864


>gnl|CDD|37884 KOG2673, KOG2673, KOG2673, Uncharacterized conserved protein,
           contains PSP domain [Function unknown].
          Length = 485

 Score = 28.1 bits (62), Expect = 6.0
 Identities = 13/76 (17%), Positives = 19/76 (25%)

Query: 299 PHFDQEKLQTIADNTLEDPHFKPHLPEPEPLPQYKEHSDRQKPSEPLAEHPHPKRKEVER 358
                E    + +N +        L  P P    K    +++  EP       K  E   
Sbjct: 313 SDSGTEVDDPLTENEVASEPRPNSLDLPVPEDPGKTSDGKERLEEPELPDIFTKDVEAGH 372

Query: 359 ELSEIEGAKKESSARK 374
              E          RK
Sbjct: 373 ASDEDSEVTSLCQKRK 388


>gnl|CDD|38255 KOG3045, KOG3045, KOG3045, Predicted RNA methylase involved in rRNA
           processing [RNA processing and modification].
          Length = 325

 Score = 28.1 bits (62), Expect = 6.0
 Identities = 25/143 (17%), Positives = 46/143 (32%), Gaps = 15/143 (10%)

Query: 330 PQYKEHSDRQKPSEPLAEHPHPKRKEVERELSEIEGAKKESSARKFFDEGSPDHSPFKGE 389
           P  K  S + K  +        KRK+ ER+L   + A+ + +  +         SP +  
Sbjct: 23  PSEKPTSSKTKEEKK-----KKKRKKGERKLKAKKAAELKENVEEPPLGSEAKSSPKENS 77

Query: 390 RNQKLDPMRGADFTDAPHAKFDATTFTESLPHVDEQTMHRFSELKERHPVEAREVLEGLQ 449
           + ++ +  +         A   A T       +  +   R    + R+          L 
Sbjct: 78  KKKRRNETKKKKEKPPEKAGAAAETEKTEATDLQAKMKKRLDGGRFRY----------LN 127

Query: 450 EKLQGTKEIKTKSLIKEAINCFL 472
           E+L      +   L KE    F 
Sbjct: 128 EQLYTGTSSEAFDLFKEDPTAFD 150


>gnl|CDD|146672 pfam04156, IncA, IncA protein.  Chlamydia trachomatis is an
           obligate intracellular bacterium that develops within a
           parasitophorous vacuole termed an inclusion. The
           inclusion is non-fusogenic with lysosomes but intercepts
           lipids from a host cell exocytic pathway. Initiation of
           chlamydial development is concurrent with modification
           of the inclusion membrane by a set of C.
           trachomatis-encoded proteins collectively designated
           Incs. One of these Incs, IncA, is functionally
           associated with the homotypic fusion of inclusions. This
           family probably includes members of the wider Inc family
           rather than just IncA.
          Length = 186

 Score = 27.8 bits (62), Expect = 7.5
 Identities = 20/64 (31%), Positives = 29/64 (45%)

Query: 80  LVEGLTSLAPYIAGAALAGKLLSFIPTPLTRLAGLALQSAPLAAGALYAYLSHKAESSIH 139
           ++ GL  +A  IA   L G  L  + + L  +A LAL    LA G L   L    +S   
Sbjct: 12  IILGLLLIASGIALLVLFGAGLGALISTLLGIALLALGLVLLALGLLCLLLKAPVQSVRP 71

Query: 140 HQIE 143
            ++E
Sbjct: 72  QKLE 75


>gnl|CDD|111851 pfam03007, UPF0089, Uncharacterized protein family (UPF0089).  This
           family of uncharacterized proteins is greatly expanded
           in Mycobacterium tuberculosis. The most conserved region
           of the proteins contains conserved histidine and
           aspartate residues suggesting a possible metal binding
           site suggestive of a protease activity (Bateman A. pers.
           obs.).
          Length = 263

 Score = 27.7 bits (62), Expect = 7.8
 Identities = 28/104 (26%), Positives = 37/104 (35%), Gaps = 21/104 (20%)

Query: 38  VINMPARSLDKL-VAPFREETHDQPNYYRGSRTDPHSVGTGAHLVEGLTSLAPYIAGAA- 95
            +N+ AR LD     P R      P      RTD  + G       GL  +A  +AG   
Sbjct: 145 GLNLLARLLDLDPDPPPRPTPPQTP--PGDPRTDLRASGILVLPAAGLGRVAGGVAGVVS 202

Query: 96  LAGKLL-----------------SFIPTPLTRLAGLALQSAPLA 122
            AG+LL                 +    P++R    A QS PL 
Sbjct: 203 TAGRLLERALIARSVALPFAAPHTPFNAPVSRARRFAAQSLPLD 246


>gnl|CDD|145649 pfam02610, Arabinose_Isome, L-arabinose isomerase.  This is a
           family of L-arabinose isomerases, AraA, EC:5.3.1.4.
           These enzymes catalyse the reaction: L-arabinose <=>
           L-ribulose. This reaction is the first step in the
           pathway of L-arabinose utilisation as a carbon source
           after entering the cell L-arabinose is converted into
           L-ribulose by the L-arabinose isomerases enzyme.
          Length = 359

 Score = 27.6 bits (62), Expect = 8.2
 Identities = 9/28 (32%), Positives = 16/28 (57%)

Query: 2   YFNAVSDEDIRDNIKEWAQRPRVSPDIK 29
             NAVSDED+   + E+     ++P++ 
Sbjct: 217 AVNAVSDEDVDALVAEYEDLYDLAPELN 244


>gnl|CDD|36921 KOG1709, KOG1709, KOG1709, Guanidinoacetate methyltransferase and
           related proteins [Amino acid transport and metabolism].
          Length = 271

 Score = 27.6 bits (61), Expect = 8.8
 Identities = 24/87 (27%), Positives = 34/87 (39%), Gaps = 17/87 (19%)

Query: 106 TPLTRLAGLALQSAPLAAGALYAYLSHKAESSIHHQIEGVDKETADALAWREAIVHTSAL 165
             L  L      +A   A  L  YLS   ++ +    +GV       + W   I+H  A 
Sbjct: 43  LLLFALGRNESPNADGNAPYLQDYLSTAEDTLLDSLGKGV------MMRWETPIMHALA- 95

Query: 166 LAPGAIASQSIAKTVASGAVLNVPFGM 192
               AI+++        G VLNV FGM
Sbjct: 96  ---EAISTKG-------GRVLNVGFGM 112


>gnl|CDD|119358 cd02879, GH18_plant_chitinase_class_V, The class V plant chitinases
           have a glycosyl hydrolase family 18 (GH18) domain, but
           lack the chitin-binding domain present in other GH18
           enzymes.  The GH18 domain of the class V chitinases has
           endochitinase activity in some cases and no catalytic
           activity in others.  Included in this family is a lectin
           found in black locust (Robinia pseudoacacia) bark, which
           binds chitin but lacks chitinase activity.  Also
           included is a chitinase-related receptor-like kinase
           (CHRK1) from tobacco (Nicotiana tabacum), with an
           N-terminal GH18 domain and a C-terminal kinase domain,
           which is thought to be part of a plant signaling
           pathway.  The GH18 domain of CHRK1 is expressed
           extracellularly where it binds chitin but lacks
           chitinase activity..
          Length = 299

 Score = 27.3 bits (61), Expect = 9.2
 Identities = 9/32 (28%), Positives = 16/32 (50%), Gaps = 1/32 (3%)

Query: 408 AKFDATTFTESLPHVDEQTMHRFSE-LKERHP 438
           A  D +T+   +   DE     F+E +K ++P
Sbjct: 34  ADLDPSTYEVVISPSDESEFSTFTETVKRKNP 65


>gnl|CDD|36175 KOG0957, KOG0957, KOG0957, PHD finger protein [General function
           prediction only].
          Length = 707

 Score = 27.4 bits (60), Expect = 9.7
 Identities = 10/40 (25%), Positives = 14/40 (35%)

Query: 319 FKPHLPEPEPLPQYKEHSDRQKPSEPLAEHPHPKRKEVER 358
           F     EP P P+Y E +   K  +  +    P     E 
Sbjct: 631 FINVPKEPAPAPEYIEDTKSPKRPKLQSPCKTPINVPAEA 670


  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
   0.314    0.132    0.388 

Gapped
Lambda     K      H
   0.267   0.0479    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,840,734
Number of extensions: 310322
Number of successful extensions: 725
Number of sequences better than 10.0: 1
Number of HSP's gapped: 725
Number of HSP's successfully gapped: 31
Length of query: 478
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 381
Effective length of database: 4,167,664
Effective search space: 1587879984
Effective search space used: 1587879984
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: 42 (22.0 bits)
S2: 59 (27.1 bits)