RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780259|ref|YP_003064672.1| 50S ribosomal protein L23
[Candidatus Liberibacter asiaticus str. psy62]
         (110 letters)



>gnl|CDD|180228 PRK05738, rplW, 50S ribosomal protein L23; Reviewed.
          Length = 92

 Score =  105 bits (265), Expect = 2e-24
 Identities = 53/105 (50%), Positives = 59/105 (56%), Gaps = 14/105 (13%)

Query: 7   YDTIISPVIAEKSTLLA-GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKV 65
           YD I  PVI EKSTLL   QN+ VF V  D++K EIK+AVE LF VKV SVNTL  KGK 
Sbjct: 1   YDVIKRPVITEKSTLLMEKQNKYVFEVAPDATKPEIKAAVEKLFGVKVESVNTLNVKGKT 60

Query: 66  KRLSRISAARSRVRSSRDMYVSRKDVKRAFVTLAKGYSIDISAGV 110
           KR  R                 R D K+A VTLA+G  ID   G 
Sbjct: 61  KRFGRRIG-------------KRSDWKKAIVTLAEGQKIDFFGGA 92


>gnl|CDD|183398 PRK12280, rplW, 50S ribosomal protein L23; Reviewed.
          Length = 158

 Score = 65.6 bits (160), Expect = 3e-12
 Identities = 37/97 (38%), Positives = 51/97 (52%), Gaps = 13/97 (13%)

Query: 10  IISPVIAEKSTLLAGQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRKGKVKRLS 69
           I  P++ EKS  L  +N   F V + ++K EIK AVE +F VKV+ VN      K KRL 
Sbjct: 7   IKKPILTEKSYSLMSKNVYTFKVDRRANKIEIKKAVEFIFKVKVLKVNIFNVDKKPKRLG 66

Query: 70  RISAARSRVRSSRDMYVSRKDVKRAFVTLAKGYSIDI 106
           R     +               K+A+VTLA+GYSI++
Sbjct: 67  RFPGFTNS-------------YKKAYVTLAEGYSINL 90


>gnl|CDD|184736 PRK14548, PRK14548, 50S ribosomal protein L23P; Provisional.
          Length = 84

 Score = 60.3 bits (147), Expect = 1e-10
 Identities = 28/62 (45%), Positives = 39/62 (62%), Gaps = 2/62 (3%)

Query: 7  YDTIISPVIAEKSTLLA-GQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIR-KGK 64
          Y  I  P++ EK+  L   +N++ F V + ++K +IK AVE LF VKV  VNTLI  KG+
Sbjct: 2  YSIIKYPLVTEKAMNLIEKENKLTFIVDRRATKPDIKRAVEELFDVKVEKVNTLITPKGE 61

Query: 65 VK 66
           K
Sbjct: 62 KK 63


>gnl|CDD|132675 TIGR03636, L23_arch, archaeal ribosomal protein L23.  This model
          describes the archaeal ribosomal protein L23P and
          rigorously excludes the bacterial counterpart L23. In
          order to capture every known instance of archaeal L23P,
          the trusted cutoff is set lower than a few of the
          highest scoring eukaryotic cytosolic ribosomal
          counterparts.
          Length = 77

 Score = 52.6 bits (127), Expect = 2e-08
 Identities = 23/51 (45%), Positives = 34/51 (66%), Gaps = 1/51 (1%)

Query: 13 PVIAEKST-LLAGQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIRK 62
          P++ EK+  L+  +N++ F V + ++K +IK AVE LF VKV  VNTLI  
Sbjct: 1  PLVTEKAMNLIEKENKLTFIVDRKATKGDIKRAVEKLFDVKVEKVNTLITP 51


>gnl|CDD|185507 PTZ00191, PTZ00191, 60S ribosomal protein L23a; Provisional.
          Length = 145

 Score = 46.6 bits (111), Expect = 1e-06
 Identities = 29/70 (41%), Positives = 40/70 (57%), Gaps = 2/70 (2%)

Query: 6   FYDTIISPVIAEKST-LLAGQNQVVFNVKKDSSKSEIKSAVEALFSVKVVSVNTLIR-KG 63
            Y  I  P+  EK+   +   N +VF V + ++K++IK AVE L+ VKVV VNTLI   G
Sbjct: 62  KYSIIKYPLTTEKAMKKIEDNNTLVFIVDQRANKTQIKKAVEKLYDVKVVKVNTLITPDG 121

Query: 64  KVKRLSRISA 73
             K   R+S 
Sbjct: 122 LKKAYIRLSP 131


>gnl|CDD|181432 PRK08453, fliD, flagellar capping protein; Validated.
          Length = 673

 Score = 28.7 bits (64), Expect = 0.32
 Identities = 15/30 (50%), Positives = 17/30 (56%)

Query: 80  SSRDMYVSRKDVKRAFVTLAKGYSIDISAG 109
           SSRD   S+ D    F T  K Y+IDI AG
Sbjct: 118 SSRDDVFSQVDTTLKFYTQGKDYAIDIKAG 147


>gnl|CDD|178741 PLN03200, PLN03200, cellulose synthase-interactive protein;
           Provisional.
          Length = 2102

 Score = 26.6 bits (59), Expect = 1.6
 Identities = 19/81 (23%), Positives = 42/81 (51%), Gaps = 7/81 (8%)

Query: 29  VFNVKKDSSKSEIKSAVEALFSV-KVVSVNTLIRKGKVKRLSRISAARSR-VRSSRDMYV 86
           +F+ ++D  +S      E +    K+++ NT   +    + +R  AA SR ++ +R +  
Sbjct: 636 IFSSRQDLCESLA--TDEIINPCIKLLTNNT---EAVATQSARALAALSRSIKENRKVSY 690

Query: 87  SRKDVKRAFVTLAKGYSIDIS 107
           + +D  +  + LAK  SI+++
Sbjct: 691 AAEDAIKPLIKLAKSSSIEVA 711


>gnl|CDD|152098 pfam11662, DUF3263, Protein of unknown function (DUF3263).  This
          family of proteins with unknown function appears to be
          restricted to Actinobacteria.
          Length = 77

 Score = 25.4 bits (56), Expect = 3.4
 Identities = 10/18 (55%), Positives = 14/18 (77%)

Query: 65 VKRLSRISAARSRVRSSR 82
          VKRL R+ ++R R RS+R
Sbjct: 60 VKRLRRLRSSRQRARSAR 77


>gnl|CDD|184599 PRK14277, PRK14277, chaperone protein DnaJ; Provisional.
          Length = 386

 Score = 25.1 bits (55), Expect = 3.9
 Identities = 9/27 (33%), Positives = 17/27 (62%)

Query: 83  DMYVSRKDVKRAFVTLAKGYSIDISAG 109
           D   + +++K+A+  LAK Y  D++ G
Sbjct: 14  DRNATEEEIKKAYRRLAKKYHPDLNPG 40


>gnl|CDD|169383 PRK08329, PRK08329, threonine synthase; Validated.
          Length = 347

 Score = 24.8 bits (54), Expect = 4.7
 Identities = 26/74 (35%), Positives = 35/74 (47%), Gaps = 12/74 (16%)

Query: 24  GQNQVVFNVKKDSS-KSEIKSAVEALFS-VKV---VSVNTLIRKGKVKRLSRISAARSRV 78
           G N+VV     DSS  + +  A+ +L   +KV   VS N    K K+  LSR+ A    V
Sbjct: 103 GINEVVI----DSSGNAALSLALYSLSEGIKVHVFVSYNA--SKEKISLLSRLGAELHFV 156

Query: 79  RSSRDMYVSRKDVK 92
              R M V  + VK
Sbjct: 157 EGDR-MEVHEEAVK 169


>gnl|CDD|180917 PRK07279, dnaE, DNA polymerase III DnaE; Reviewed.
          Length = 1034

 Score = 25.0 bits (55), Expect = 4.9
 Identities = 12/42 (28%), Positives = 23/42 (54%), Gaps = 1/42 (2%)

Query: 27  QVVFNVKKDSSKSE-IKSAVEALFSVKVVSVNTLIRKGKVKR 67
            V +++  + S S+ I  A+E  F V  +S+NT+    K++ 
Sbjct: 704 AVFYDIMLNYSSSDYITDALEFGFEVAKLSINTIPYHDKIEN 745


>gnl|CDD|184602 PRK14280, PRK14280, chaperone protein DnaJ; Provisional.
          Length = 376

 Score = 24.7 bits (54), Expect = 5.4
 Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 8/36 (22%)

Query: 80  SSRDMY--------VSRKDVKRAFVTLAKGYSIDIS 107
           + RD Y         S+ ++K+A+  L+K Y  DI+
Sbjct: 2   AKRDYYEVLGVSKSASKDEIKKAYRKLSKKYHPDIN 37



 Score = 24.3 bits (53), Expect = 7.5
 Identities = 10/20 (50%), Positives = 11/20 (55%)

Query: 29 VFNVKKDSSKSEIKSAVEAL 48
          V  V K +SK EIK A   L
Sbjct: 9  VLGVSKSASKDEIKKAYRKL 28


>gnl|CDD|172778 PRK14290, PRK14290, chaperone protein DnaJ; Provisional.
          Length = 365

 Score = 24.5 bits (53), Expect = 6.3
 Identities = 11/27 (40%), Positives = 17/27 (62%)

Query: 83  DMYVSRKDVKRAFVTLAKGYSIDISAG 109
           D   S++D+K+AF  LAK +  D+  G
Sbjct: 12  DRNASQEDIKKAFRELAKKWHPDLHPG 38


>gnl|CDD|162033 TIGR00770, Dcu, anaerobic c4-dicarboxylate membrane transporter
           family protein.  These proteins are members of th
           C4-Dicarboxylate Uptake (Dcu) Family (TC 2.A.13). Most
           proteins in this family have 12 GES predicted
           transmembrane regions; however one member has 10
           experimentally determined transmembrane regions with
           both the N- and C-termini localized to the periplasm.
           The two Escherichia coli proteins, DcuA and DcuB,
           transport aspartate, malate, fumarate and succinate, and
           function as antiporters with any two of these
           substrates. Since DcuA is encoded in an operon with the
           gene for aspartase, and DcuB is encoded in an operon
           with the gene for fumarase, their physiological
           functions may be to catalyze aspartate:fumarate and
           fumarate:malate exchange during the anaerobic
           utilization of aspartate and fumarate, respectively.
          Length = 430

 Score = 24.3 bits (53), Expect = 7.1
 Identities = 10/26 (38%), Positives = 16/26 (61%)

Query: 7   YDTIISPVIAEKSTLLAGQNQVVFNV 32
           Y TI++P +    T+LAG   VV++ 
Sbjct: 83  YITILAPSVTYFLTILAGTGHVVYST 108


>gnl|CDD|184385 PRK13905, murB, UDP-N-acetylenolpyruvoylglucosamine reductase;
           Provisional.
          Length = 298

 Score = 24.3 bits (54), Expect = 7.6
 Identities = 8/18 (44%), Positives = 11/18 (61%)

Query: 53  VVSVNTLIRKGKVKRLSR 70
           + SV  L R G++K LS 
Sbjct: 146 LESVEVLDRDGEIKTLSN 163


>gnl|CDD|173334 PTZ00037, PTZ00037, DnaJ_C chaperone protein; Provisional.
          Length = 421

 Score = 24.0 bits (52), Expect = 8.2
 Identities = 10/20 (50%), Positives = 12/20 (60%)

Query: 29 VFNVKKDSSKSEIKSAVEAL 48
          V N+ KD + SEIK A   L
Sbjct: 33 VLNLSKDCTTSEIKKAYRKL 52


  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
   0.318    0.130    0.329 

Gapped
Lambda     K      H
   0.267   0.0780    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,603,660
Number of extensions: 84234
Number of successful extensions: 238
Number of sequences better than 10.0: 1
Number of HSP's gapped: 233
Number of HSP's successfully gapped: 39
Length of query: 110
Length of database: 5,994,473
Length adjustment: 76
Effective length of query: 34
Effective length of database: 4,352,265
Effective search space: 147977010
Effective search space used: 147977010
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 (21.8 bits)
S2: 50 (22.9 bits)