RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781191|ref|YP_003065604.1| hypothetical protein
CLIBASIA_05490 [Candidatus Liberibacter asiaticus str. psy62]
         (165 letters)



>gnl|CDD|151373 pfam10926, DUF2800, Protein of unknown function (DUF2800).  This is
           a family of uncharacterized proteins found in bacteria
           and viruses. Some members of this family are annotated
           as being Phi APSE P51-like proteins.
          Length = 363

 Score =  108 bits (272), Expect = 7e-25
 Identities = 49/146 (33%), Positives = 79/146 (54%), Gaps = 11/146 (7%)

Query: 6   CRFCRAKPRCGALAVKALST----FSEHMQILSNRQLSQVMNVLPLIETWMKGVKEEALN 61
           CRFC+AK  C A A   L+     F +    L++ +L++++    L+E W K V+  AL+
Sbjct: 215 CRFCKAKATCRARAQAVLNLAKYDFEDPTLDLTDEELAELLEKADLLEKWAKDVEAYALD 274

Query: 62  VLSSGEDLPNYELKEGRKGSRTYNNDNQVEQLLMRE-LGDEA-YNRTLLSPTETEQLVKR 119
              +G+++P Y+L EGR  +R + ++  V   L    L DE  Y + L+SPT+ E+L+ +
Sbjct: 275 EARNGKEVPGYKLVEGR-SNRKWTDEEAVAAALKAAGLKDEDIYKKKLISPTQAEKLLGK 333

Query: 120 KKVSETTWEQLQKFITRKDGKQVIVP 145
           KK  E     L   I +  GK  +VP
Sbjct: 334 KKFKEL----LGALIVKPPGKPTLVP 355


>gnl|CDD|150843 pfam10232, Med8, Mediator of RNA polymerase II transcription
           complex subunit 8.  Arc32, or Med8, is one of the
           subunits of the Mediator complex of RNA polymerase II.
           The region conserved contains two alpha helices
           putatively necessary for binding to other subunits
           within the core of the Mediator complex. The N-terminus
           of Med8 binds to the essential core Head part of
           Mediator and the C-terminus hinges to Med18 on the
           non-essential part of the Head that also includes Med20.
          Length = 226

 Score = 30.6 bits (69), Expect = 0.19
 Identities = 19/85 (22%), Positives = 32/85 (37%), Gaps = 5/85 (5%)

Query: 44  VLPLIETWMKGVKEEALNVLSSGEDLPNYELKEGRKGSRTYNNDNQVEQLLMRELGDEAY 103
             P +E WMK  +++A N           E+   ++     N  ++V   L  E   E+ 
Sbjct: 99  PDPEVEEWMKQARQKAENSTKDTAAKQEVEIDILQQNKEVSNWLDKV-TKLREEWEFESS 157

Query: 104 NRT----LLSPTETEQLVKRKKVSE 124
           +R          +T QLV   K  +
Sbjct: 158 HRVEIEQTSEEEDTNQLVAAVKDGK 182


>gnl|CDD|151744 pfam11303, DUF3105, Protein of unknown function (DUF3105).  Some
           members in this family of proteins are annotated as
           membrane proteins however this cannot be confirmed.
           Currently no function is known.
          Length = 130

 Score = 29.6 bits (67), Expect = 0.38
 Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 9/54 (16%)

Query: 83  TYN---NDNQVEQLLMRELGDEAYNRTLLSPTETEQLVKRKKVSETTWEQLQKF 133
           TY+     ++VE+L  + L      R LLSP           V+ T W +  + 
Sbjct: 55  TYDPDLPPDEVEKL--KALAAGCLPRVLLSPYPG----LDSPVALTAWGRQLEL 102


>gnl|CDD|184618 PRK14318, glmM, phosphoglucosamine mutase; Provisional.
          Length = 448

 Score = 27.2 bits (61), Expect = 2.2
 Identities = 12/23 (52%), Positives = 14/23 (60%), Gaps = 2/23 (8%)

Query: 96  RELGDEAYNRTLLSPTETEQLVK 118
            ELGD    R LL P+ TE LV+
Sbjct: 401 AELGDTG--RVLLRPSGTEPLVR 421


>gnl|CDD|161897 TIGR00474, selA, seryl-tRNA(sec) selenium transferase.  In
           bacteria, the incorporation of selenocysteine as the
           21st amino acid, encoded by TGA, requires several
           elements: SelC is the tRNA itself, SelD acts as a donor
           of reduced selenium, SelA modifies a serine residue on
           SelC into selenocysteine, and SelB is a
           selenocysteine-specific translation elongation factor.
           3-prime or 5-prime non-coding elements of mRNA have been
           found as probable structures for directing
           selenocysteine incorporation. This model describes SelA.
           This model excludes homologs that appear to differ in
           function from Frankia alni, Helicobacter pylori,
           Methanococcus jannaschii and other archaea, and so on.
          Length = 454

 Score = 26.8 bits (60), Expect = 2.6
 Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 4/31 (12%)

Query: 72  YELKEGRKGSRTYNNDNQVEQLLMRELGDEA 102
           Y+L+ G++GSR     + VE LL    G E 
Sbjct: 113 YDLETGKRGSR----YSHVEGLLCELTGAED 139


>gnl|CDD|106194 PRK13232, nifH, nitrogenase reductase; Reviewed.
          Length = 273

 Score = 26.9 bits (59), Expect = 2.8
 Identities = 19/95 (20%), Positives = 46/95 (48%), Gaps = 16/95 (16%)

Query: 81  SRTYNNDNQVEQLLMRELGDEAYNRTLLSPTETEQLVKRKKVSETT-------WEQLQKF 133
           SR  + + ++ +   ++LG +     L+     + +V+R +++  T         Q +++
Sbjct: 183 SRNVDGERELLEAFAKKLGSQ-----LIHFVPRDNIVQRAEINRKTVIDFDPESNQAKEY 237

Query: 134 ITRKDGKQ----VIVPCDLPVNHLKANISEFSVLK 164
           +T     Q    ++VP  LP+  L+A + EF +++
Sbjct: 238 LTLAHNVQNNDKLVVPTPLPMEELEAMMVEFGIVE 272


>gnl|CDD|180894 PRK07226, PRK07226, fructose-bisphosphate aldolase; Provisional.
          Length = 267

 Score = 26.7 bits (60), Expect = 3.1
 Identities = 8/18 (44%), Positives = 12/18 (66%)

Query: 130 LQKFITRKDGKQVIVPCD 147
           L++   R+ G+ VIVP D
Sbjct: 10  LERIFNRRTGRTVIVPMD 27


>gnl|CDD|177868 PLN02222, PLN02222, phosphoinositide phospholipase C 2.
          Length = 581

 Score = 26.5 bits (58), Expect = 3.4
 Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 1/44 (2%)

Query: 26  FSEHMQILSNRQLSQVMNVLPLIETWMKGVKEEALNVL-SSGED 68
           F+ H   L+  QLS   + +P+I+   KGV+   L++  +S +D
Sbjct: 115 FTGHNSYLTGNQLSSDCSEVPIIDALKKGVRVIELDIWPNSDKD 158


>gnl|CDD|178827 PRK00053, alr, alanine racemase; Reviewed.
          Length = 363

 Score = 26.3 bits (59), Expect = 4.0
 Identities = 9/34 (26%), Positives = 15/34 (44%), Gaps = 4/34 (11%)

Query: 123 SETTWEQLQKFITRKDGKQVIVPCDLPVNHLKAN 156
           +  T +QL +F   +     +     P+ HL AN
Sbjct: 170 NSYTEQQLNRF---EAALAGLPGKGKPLRHL-AN 199


>gnl|CDD|182335 PRK10252, entF, enterobactin synthase subunit F; Provisional.
          Length = 1296

 Score = 26.2 bits (58), Expect = 4.0
 Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 24/76 (31%)

Query: 41  VMNVLPLIETWMKGVKEEALNVLSSGEDLP------NYELKEGRKGSRTYNNDNQVEQLL 94
           V+NVLPL            ++ +++ E LP        +LK+ R+  R Y      EQ++
Sbjct: 293 VLNVLPL-----------RVH-IAAQETLPELATRLAAQLKKMRRHQR-Y----DAEQIV 335

Query: 95  MRELGDEAYNRTLLSP 110
            R+ G  A +  L  P
Sbjct: 336 -RDSGRAAGDEPLFGP 350


>gnl|CDD|131231 TIGR02176, pyruv_ox_red, pyruvate:ferredoxin (flavodoxin)
           oxidoreductase, homodimeric.  This model represents a
           single chain form of pyruvate:ferredoxin (or flavodoxin)
           oxidoreductase. This enzyme may transfer electrons to
           nitrogenase in nitrogen-fixing species. Portions of this
           protein are homologous to gamma subunit of the four
           subunit pyruvate:ferredoxin (flavodoxin) oxidoreductase.
          Length = 1165

 Score = 25.9 bits (57), Expect = 4.9
 Identities = 10/26 (38%), Positives = 15/26 (57%)

Query: 17  ALAVKALSTFSEHMQILSNRQLSQVM 42
           A+A  ALS F +H  +++ RQ    M
Sbjct: 111 AIAAHALSIFGDHQDVMAARQTGFAM 136


>gnl|CDD|119297 pfam10777, YlaC, Extracytoplasmic function sigma factor YlaC.
           YlaC, regulated by YlaA, is important in oxidative
           stress resistance. It contributes to hydrogen peroxide
           resistance in Bacillus subtilis.
          Length = 156

 Score = 25.8 bits (57), Expect = 6.0
 Identities = 10/37 (27%), Positives = 17/37 (45%)

Query: 101 EAYNRTLLSPTETEQLVKRKKVSETTWEQLQKFITRK 137
           E YN   +S    ++++    V +    QL+K I  K
Sbjct: 103 EWYNTRAVSQQLIDEILNSPNVPDEQKAQLKKIIATK 139


>gnl|CDD|166345 PLN02704, PLN02704, flavonol synthase.
          Length = 335

 Score = 25.1 bits (55), Expect = 8.9
 Identities = 11/30 (36%), Positives = 16/30 (53%)

Query: 51  WMKGVKEEALNVLSSGEDLPNYELKEGRKG 80
           +++GV ++    LS G  L   ELKE   G
Sbjct: 165 YLRGVADKLFKTLSLGLGLEEDELKEAVGG 194


>gnl|CDD|177331 PHA02004, PHA02004, capsid protein.
          Length = 332

 Score = 25.2 bits (55), Expect = 9.4
 Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 2/35 (5%)

Query: 90  VEQLLMRELGDEAYNR--TLLSPTETEQLVKRKKV 122
           VE L+ R+LGD  Y+   TL+SP     L++  K+
Sbjct: 182 VETLIKRDLGDAVYSEGLTLVSPRIFSLLLEHDKL 216


  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
   0.315    0.130    0.371 

Gapped
Lambda     K      H
   0.267   0.0656    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,541,360
Number of extensions: 147800
Number of successful extensions: 346
Number of sequences better than 10.0: 1
Number of HSP's gapped: 343
Number of HSP's successfully gapped: 20
Length of query: 165
Length of database: 5,994,473
Length adjustment: 86
Effective length of query: 79
Effective length of database: 4,136,185
Effective search space: 326758615
Effective search space used: 326758615
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: 53 (24.3 bits)