RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780589|ref|YP_003065002.1| hypothetical protein
CLIBASIA_02380 [Candidatus Liberibacter asiaticus str. psy62]
         (239 letters)



>gnl|CDD|32849 COG3034, COG3034, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 298

 Score =  217 bits (553), Expect = 3e-57
 Identities = 96/234 (41%), Positives = 133/234 (56%), Gaps = 3/234 (1%)

Query: 1   MTNRYNILLFALFIFLNGCHHSRSLI-DKAEHPLSENLIISMQKKRTSPFHPTVIRIFKN 59
           M          L   L  C     L+  K ++  S  L +  + K        ++RIFK 
Sbjct: 1   MLFVLLKAALILAELLALCLSQGLLLVGKDKYFWSSELPVKNEAKGLYREKVVLVRIFKE 60

Query: 60  ENILEIWKRNVDAEYVLLKEYKICAWSGTFGPKIETGDEQAPEGFYYIGWNNLNPNSKYF 119
           E  LE+++++    Y LL+ YKIC WSG  GPK   GD + PEGFY +    LNP+S Y+
Sbjct: 61  ERKLELYEKD-GNIYKLLRSYKICLWSGKLGPKQREGDLKTPEGFYRLTRKQLNPDSYYY 119

Query: 120 LSINIGFPNEFDKAHNRTGADLMIHGECASAGCYAMNNKQMQEIYAIVRDSLRGNMQSHI 179
           LSINIG+PN +DKA  RTG  +MIHG C S GCY+M + Q+ EIY  V  +L+G  Q  +
Sbjct: 120 LSINIGYPNAYDKALGRTGGGIMIHGACLSDGCYSMTDAQIDEIYGCVAKALQG-GQESV 178

Query: 180 QIQAFPFRMTSKNMQLYQNNPNYSFWNMLKLGHDYFEKNHQEPFIQIINKQYVF 233
           Q+ A PFRMT +NM  ++ +P +SFW  LK G+D FE     P + + + +YVF
Sbjct: 179 QVVADPFRMTIENMVRHRLSPLFSFWKALKPGYDNFEVTFYPPTVSVCDGRYVF 232


>gnl|CDD|146395 pfam03734, YkuD, L,D-transpeptidase catalytic domain.  This family
           of proteins are found in a range of bacteria. It has
           been shown that this domain can act as an
           L,D-transpeptidase that gives rise to an alternative
           pathway for peptidoglycan cross-linking. This gives
           bacteria resistance to beta-lactam antibiotics that
           inhibit PBPs which usually carry out the cross-linking
           reaction. The conserved region contains a conserved
           histidine and cysteine, with the cysteine thought to be
           an active site residue. Several members of this family
           contain peptidoglycan binding domains. The molecular
           structure of YkuD protein shows this domain has a novel
           tertiary fold consisting of a beta-sandwich with two
           mixed sheets, one containing five strands and the other,
           six strands. The two beta-sheets form a cradle capped by
           an alpha-helix. This family was formerly called the
           ErfK/YbiS/YcfS/YnhG family, but is now named after the
           first protein of known structure.
          Length = 122

 Score = 58.7 bits (142), Expect = 1e-09
 Identities = 27/129 (20%), Positives = 44/129 (34%), Gaps = 25/129 (19%)

Query: 51  PTVIRIFKNE-NILEIWKRNVDAEYVLLKEYKICAWSGTFGPKIETGDEQAPEGFYYIGW 109
             VI +  +E  +L +++        L+  Y +    G        GD   P G + I  
Sbjct: 1   DRVIVVDLSEQRLLLLYENGK-----LVLTYPVS--VGR-------GDTPTPLGTFTITE 46

Query: 110 NNLNPNSKYFLSINIGFPNEFDKAHNRTGADLMIH----------GECASAGCYAMNNKQ 159
              NP         +G+    D      G  + IH          G   S GC  ++N+ 
Sbjct: 47  KVENPTWAPGPGNGLGYVKFLDPWAFPNGGGIYIHGTGTPDLFSGGAPRSHGCIRLSNED 106

Query: 160 MQEIYAIVR 168
            +E+Y  V 
Sbjct: 107 AKELYDWVL 115


>gnl|CDD|33259 COG3456, COG3456, Uncharacterized conserved protein, contains FHA
           domain [Signal transduction mechanisms].
          Length = 430

 Score = 28.4 bits (63), Expect = 1.6
 Identities = 11/58 (18%), Positives = 22/58 (37%), Gaps = 7/58 (12%)

Query: 159 QMQEIYAIVRDSLRGNMQSHIQIQAFPFRMTSKNMQLYQNNPNYSFWNMLKLGHDYFE 216
            ++E    +R  + G +    Q      R+    ++  ++NP       L+   DY E
Sbjct: 264 FLEEAGRTLRACIEGLLDLLRQRAKGSARLLQTMLRPSEDNP-------LRFAPDYDE 314


>gnl|CDD|31566 COG1376, ErfK, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 232

 Score = 28.3 bits (62), Expect = 1.9
 Identities = 7/25 (28%), Positives = 14/25 (56%)

Query: 145 GECASAGCYAMNNKQMQEIYAIVRD 169
           G+  S GC  ++N+  +++Y  V  
Sbjct: 198 GKAVSHGCIRLSNQDAKDLYNRVPV 222


>gnl|CDD|36800 KOG1587, KOG1587, KOG1587, Cytoplasmic dynein intermediate chain
           [Cytoskeleton].
          Length = 555

 Score = 27.3 bits (60), Expect = 4.0
 Identities = 20/90 (22%), Positives = 30/90 (33%), Gaps = 9/90 (10%)

Query: 47  SPFHPTVIRIFKNENILEIWKRNVDAEYVLLKEYKICA-------WSGTFGPKIETGDEQ 99
           SP  P V      +  L+IW    D E  +L + K+C+       WS   G  +  GD  
Sbjct: 450 SPTRPAVFATVDGDGNLDIWDLLQDDEEPVLSQ-KVCSPALTRVRWSPN-GKLLAVGDAN 507

Query: 100 APEGFYYIGWNNLNPNSKYFLSINIGFPNE 129
                  +  +   P+          F  E
Sbjct: 508 GTTHILKLSESLAVPSPNEKALFAHMFERE 537


>gnl|CDD|36310 KOG1094, KOG1094, KOG1094, Discoidin domain receptor DDR1 [Signal
           transduction mechanisms].
          Length = 807

 Score = 26.9 bits (59), Expect = 5.0
 Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 7/42 (16%)

Query: 103 GFYYIGWNNLNPNSKYFLSINIGFPNEFDKAHNRTGADLMIH 144
           G+ Y+GW N +  + Y   + I F  EFD+  N +   + +H
Sbjct: 246 GYDYVGWRNDSFTNGY---VEIEF--EFDELRNFS--AMQVH 280


>gnl|CDD|36882 KOG1669, KOG1669, KOG1669, Predicted mRNA cap-binding protein
           related to eIF-4E [Translation, ribosomal structure and
           biogenesis].
          Length = 208

 Score = 26.5 bits (58), Expect = 6.3
 Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 3/40 (7%)

Query: 35  ENLIISMQKKRTSPFHPT---VIRIFKNENILEIWKRNVD 71
           ENL++++  ++          V  +  NE+I+ IW RN  
Sbjct: 123 ENLLLALCGEQFKVGEEICGAVGSVRFNEDIISIWNRNAS 162


>gnl|CDD|32326 COG2143, COG2143, Thioredoxin-related protein [Posttranslational
          modification, protein turnover, chaperones].
          Length = 182

 Score = 26.1 bits (57), Expect = 8.4
 Identities = 12/83 (14%), Positives = 26/83 (31%), Gaps = 8/83 (9%)

Query: 7  ILLFALFIFLNGCHHSRSLIDKAEHPLSENLIISMQKK-------RTSPFHPTVIR-IFK 58
          I+L  + +FL+ C  +       +       I    K            +     + +  
Sbjct: 7  IVLLIISLFLSACKSNNEKRSNIDVFDDNKSISPNDKYLLLMFESNGCSYCERFKKDLKN 66

Query: 59 NENILEIWKRNVDAEYVLLKEYK 81
           + + E  K +  A Y+ +   K
Sbjct: 67 VKRLREYLKEHFSAYYLNISYSK 89


  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
   0.323    0.138    0.431 

Gapped
Lambda     K      H
   0.267   0.0630    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,047,300
Number of extensions: 157735
Number of successful extensions: 347
Number of sequences better than 10.0: 1
Number of HSP's gapped: 343
Number of HSP's successfully gapped: 17
Length of query: 239
Length of database: 6,263,737
Length adjustment: 91
Effective length of query: 148
Effective length of database: 4,297,318
Effective search space: 636003064
Effective search space used: 636003064
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 56 (25.6 bits)