BLASTP 2.2.22 [Sep-27-2009]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= gi|254780766|ref|YP_003065179.1| recombination protein F
[Candidatus Liberibacter asiaticus str. psy62]
         (375 letters)

Database: las_proteome 
           1233 sequences; 328,796 total letters

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



>gi|254780766|ref|YP_003065179.1| recombination protein F [Candidatus Liberibacter asiaticus str.
           psy62]
          Length = 375

 Score =  767 bits (1981), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 375/375 (100%), Positives = 375/375 (100%)

Query: 1   MTNRIKIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRAS 60
           MTNRIKIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRAS
Sbjct: 1   MTNRIKIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRAS 60

Query: 61  YADVTRIGSPSFFSTFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHL 120
           YADVTRIGSPSFFSTFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHL
Sbjct: 61  YADVTRIGSPSFFSTFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHL 120

Query: 121 RISWLVPSMDRIFSGLSMERRRFLDRMVFAIDPRHRRRMIDFERLMRGRNRLLTEGYFDS 180
           RISWLVPSMDRIFSGLSMERRRFLDRMVFAIDPRHRRRMIDFERLMRGRNRLLTEGYFDS
Sbjct: 121 RISWLVPSMDRIFSGLSMERRRFLDRMVFAIDPRHRRRMIDFERLMRGRNRLLTEGYFDS 180

Query: 181 SWCSSIEAQMAELGVKINIARVEMINALSSLIMEYVQKENFPHIKLSLTGFLDGKFDQSF 240
           SWCSSIEAQMAELGVKINIARVEMINALSSLIMEYVQKENFPHIKLSLTGFLDGKFDQSF
Sbjct: 181 SWCSSIEAQMAELGVKINIARVEMINALSSLIMEYVQKENFPHIKLSLTGFLDGKFDQSF 240

Query: 241 CALKEEYAKKLFDGRKMDSMSRRTLIGPHRSDLIVDYCDKAITIAHGSTGEQKVVLVGIF 300
           CALKEEYAKKLFDGRKMDSMSRRTLIGPHRSDLIVDYCDKAITIAHGSTGEQKVVLVGIF
Sbjct: 241 CALKEEYAKKLFDGRKMDSMSRRTLIGPHRSDLIVDYCDKAITIAHGSTGEQKVVLVGIF 300

Query: 301 LAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTGTDKSVFDSLNE 360
           LAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTGTDKSVFDSLNE
Sbjct: 301 LAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTGTDKSVFDSLNE 360

Query: 361 TAKFMRISNHQALCI 375
           TAKFMRISNHQALCI
Sbjct: 361 TAKFMRISNHQALCI 375


>gi|254780640|ref|YP_003065053.1| hypothetical protein CLIBASIA_02635 [Candidatus Liberibacter
          asiaticus str. psy62]
          Length = 110

 Score = 34.3 bits (77), Expect = 0.003,   Method: Composition-based stats.
 Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 1/54 (1%)

Query: 6  KIKFLNISEFRNYASLRLVFDAQH-TIFVGDNGVGKTNILEAISFLSPGRGFRR 58
          K+  + IS FR +  ++ +  A H TI  G NG GK+++ EAI +L  G   RR
Sbjct: 28 KLLDIEISHFRGFTEIQKIEFADHLTIVNGQNGYGKSSLSEAIEWLFYGYTQRR 81


>gi|255764514|ref|YP_003065586.2| DNA repair protein RecN [Candidatus Liberibacter asiaticus str.
          psy62]
          Length = 554

 Score = 31.2 bits (69), Expect = 0.027,   Method: Compositional matrix adjust.
 Identities = 15/36 (41%), Positives = 23/36 (63%)

Query: 20 SLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRG 55
          SL + F A  +I  GD G GK+ +L+A+  ++ GRG
Sbjct: 14 SLDIDFSAGLSILSGDTGSGKSILLDALILVTGGRG 49


>gi|254780795|ref|YP_003065208.1| homoserine kinase [Candidatus Liberibacter asiaticus str. psy62]
          Length = 316

 Score = 28.1 bits (61), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 4/72 (5%)

Query: 183 CSSIEAQMAELGVKINIARVEMINALSSLIMEYVQKENFPHIKLSLTGFLDGKFDQSFCA 242
           C  I + +A +  K     +   N LS L ++++  + F  +   L      + D  FC 
Sbjct: 118 CEEIGSMLASMHQKTKNFHLYRKNTLSPLNLKFLWAKCFDKVDEDLKK----EIDHEFCF 173

Query: 243 LKEEYAKKLFDG 254
           LKE + K L  G
Sbjct: 174 LKESWPKNLPTG 185


>gi|254780270|ref|YP_003064683.1| ATP-dependent protease La [Candidatus Liberibacter asiaticus str.
           psy62]
          Length = 820

 Score = 27.3 bits (59), Expect = 0.44,   Method: Compositional matrix adjust.
 Identities = 14/33 (42%), Positives = 21/33 (63%), Gaps = 1/33 (3%)

Query: 32  FVGDNGVGKTNILEAISFLSPGRGFRRASYADV 64
           FVG  GVGKT++ ++I+  + GR + R S   V
Sbjct: 371 FVGPPGVGKTSLAQSIAKAT-GRQYVRMSLGGV 402


>gi|254780877|ref|YP_003065290.1| ATP-dependent Clp protease, ATP-binding subunit protein [Candidatus
           Liberibacter asiaticus str. psy62]
          Length = 853

 Score = 26.9 bits (58), Expect = 0.57,   Method: Compositional matrix adjust.
 Identities = 9/20 (45%), Positives = 15/20 (75%)

Query: 29  HTIFVGDNGVGKTNILEAIS 48
           + + +GD GVGKT I+E ++
Sbjct: 201 NPVLIGDPGVGKTAIIEGLA 220



 Score = 23.5 bits (49), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 8/20 (40%), Positives = 16/20 (80%)

Query: 31  IFVGDNGVGKTNILEAISFL 50
           +F+G  GVGKT ++++++ L
Sbjct: 602 MFLGPTGVGKTELVKSLARL 621


>gi|254780552|ref|YP_003064965.1| Holliday junction DNA helicase RuvB [Candidatus Liberibacter
          asiaticus str. psy62]
          Length = 334

 Score = 26.6 bits (57), Expect = 0.81,   Method: Compositional matrix adjust.
 Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 1/40 (2%)

Query: 29 HTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTRIG 68
          H +FVG  G+GKT + + ++    G  FR  S   + + G
Sbjct: 56 HVLFVGPPGLGKTTLAQVVAR-ELGVNFRSTSGPVIAKAG 94


>gi|255764467|ref|YP_003064798.2| Type I secretion system ATPase, PrtD [Candidatus Liberibacter
           asiaticus str. psy62]
          Length = 565

 Score = 26.2 bits (56), Expect = 0.98,   Method: Compositional matrix adjust.
 Identities = 12/35 (34%), Positives = 21/35 (60%), Gaps = 3/35 (8%)

Query: 304 ARLISNTTGFAPILLLDEISAHLDEDKRNALFRIV 338
           +R+I+N      ILL+DE   HLD + +N  + ++
Sbjct: 478 SRIIANNPA---ILLMDEPLYHLDNEAKNNFYTLL 509


>gi|254780611|ref|YP_003065024.1| RNA polymerase factor sigma-32 [Candidatus Liberibacter asiaticus
           str. psy62]
          Length = 302

 Score = 26.2 bits (56), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 9/24 (37%), Positives = 15/24 (62%)

Query: 39  GKTNILEAISFLSPGRGFRRASYA 62
           G   +++A+    P RGFR A+Y+
Sbjct: 82  GNIGLMQAVKKFDPERGFRLATYS 105


>gi|254780999|ref|YP_003065412.1| NAD synthetase [Candidatus Liberibacter asiaticus str. psy62]
          Length = 562

 Score = 25.8 bits (55), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 19/89 (21%), Positives = 39/89 (43%), Gaps = 8/89 (8%)

Query: 157 RRMIDFERLMRGRNRLLTEGYFD---SSWCSSIEAQMAELGVKINIARVEMINALSSLIM 213
           ++ + F+         +TE ++D   S W    +   + + + +     +  NA    + 
Sbjct: 226 QQQLAFQMKHFSEQNFMTEWHYDQQLSQWNYMSDDSASTMYIPLQEEEADY-NACVLSLR 284

Query: 214 EYVQKENFPHIKLSLTGFLDGKFDQSFCA 242
           +YVQK NF  + + L+G +D     + CA
Sbjct: 285 DYVQKNNFHKVIIGLSGGIDS----ALCA 309


>gi|254780193|ref|YP_003064606.1| lipid A ABC exporter family, fused ATPase and inner membrane
           subunits [Candidatus Liberibacter asiaticus str. psy62]
          Length = 528

 Score = 25.8 bits (55), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 9/27 (33%), Positives = 19/27 (70%)

Query: 314 APILLLDEISAHLDEDKRNALFRIVTD 340
           +PILLLDE+ + LD +    +++++ +
Sbjct: 445 SPILLLDEMGSALDIENEQKIWKVLRE 471



 Score = 24.3 bits (51), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 12/25 (48%), Positives = 14/25 (56%), Gaps = 1/25 (4%)

Query: 32  FVGDNGVGKTNILEAI-SFLSPGRG 55
            VGD+G GKT+I   I  F  P  G
Sbjct: 321 LVGDSGAGKTSIFSLILRFYDPCSG 345


>gi|254780163|ref|YP_003064576.1| ATP-dependent Clp protease ATP-binding subunit [Candidatus
           Liberibacter asiaticus str. psy62]
          Length = 798

 Score = 25.8 bits (55), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 10/20 (50%), Positives = 14/20 (70%)

Query: 29  HTIFVGDNGVGKTNILEAIS 48
           + ++VGD GVGKT I E  +
Sbjct: 227 NPLYVGDPGVGKTAIAEGFA 246


>gi|254780538|ref|YP_003064951.1| ABC transporter, nucleotide binding/ATPase protein (iron)
          [Candidatus Liberibacter asiaticus str. psy62]
          Length = 280

 Score = 25.4 bits (54), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 4/52 (7%)

Query: 5  IKIKFLNISEFRNYASLRLV--FDAQHTI--FVGDNGVGKTNILEAISFLSP 52
          +++K ++++    Y +L  V  F  ++TI   +G NG GK+ + +AI  L P
Sbjct: 12 LELKDISVTYPNGYCALEDVNLFIPENTITALIGLNGAGKSTLFQAIMGLIP 63


>gi|254780874|ref|YP_003065287.1| peptide chain release factor 1 [Candidatus Liberibacter asiaticus
           str. psy62]
          Length = 357

 Score = 25.0 bits (53), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 11/63 (17%)

Query: 218 KENFPHIKLSLTGFLDGKFDQSFCALKEEYA--------KKLFDGRKMDSMSRRTLIGPH 269
           K  F  I+L ++   +     ++  L EEYA          ++D +K +     T+IG H
Sbjct: 13  KNRFAEIELRMS---ESPSVDAYIKLTEEYAAISPIISKISIYDQKKQEEQDLHTVIGDH 69

Query: 270 RSD 272
            SD
Sbjct: 70  NSD 72


>gi|254780709|ref|YP_003065122.1| cell division protein [Candidatus Liberibacter asiaticus str.
           psy62]
          Length = 321

 Score = 24.3 bits (51), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 11/43 (25%)

Query: 29  HTIFV-GDNGVGKTNILEAIS----------FLSPGRGFRRAS 60
           H I V G NGVGKT ++  +S           L+ G  FR A+
Sbjct: 112 HVILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAA 154


>gi|254781123|ref|YP_003065536.1| putative ABC transporter, ATP-binding protein [Candidatus
           Liberibacter asiaticus str. psy62]
          Length = 610

 Score = 24.3 bits (51), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 1/26 (3%)

Query: 32  FVGDNGVGKTNILEAISF-LSPGRGF 56
            VG NG GKT +L+ ++  + P  GF
Sbjct: 315 IVGPNGAGKTTLLKLLTGKIKPDCGF 340


>gi|255764516|ref|YP_003084344.1| hypothetical protein CLIBASIA_05532 [Candidatus Liberibacter
           asiaticus str. psy62]
          Length = 341

 Score = 24.3 bits (51), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 9/18 (50%), Positives = 12/18 (66%)

Query: 341 IGSQIFMTGTDKSVFDSL 358
           I  Q F+ GTD S+FD +
Sbjct: 227 INGQCFVKGTDTSIFDEI 244


>gi|254780559|ref|YP_003064972.1| thiamine transporter ATP-binding subunit [Candidatus Liberibacter
           asiaticus str. psy62]
          Length = 234

 Score = 24.3 bits (51), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 2/59 (3%)

Query: 315 PILLLDEISAHLDEDKRNALFRIVTDIGS--QIFMTGTDKSVFDSLNETAKFMRISNHQ 371
           PILLLDE  A  D   R+ +  ++  +    Q+ +     ++ DS+    +F+ I+  Q
Sbjct: 149 PILLLDEPFAVFDPALRHEILGLLKQVCDERQLTLLMISHNLEDSMQIATRFIVIAGGQ 207


>gi|254781047|ref|YP_003065460.1| AFG1-family ATPase [Candidatus Liberibacter asiaticus str. psy62]
          Length = 404

 Score = 23.9 bits (50), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 9/26 (34%), Positives = 13/26 (50%)

Query: 277 YCDKAITIAHGSTGEQKVVLVGIFLA 302
           YC       HG  G+ K +L+ +F A
Sbjct: 63  YCSMQGIYLHGDVGQGKSMLMNLFFA 88


>gi|254780947|ref|YP_003065360.1| transcription-repair coupling factor [Candidatus Liberibacter
           asiaticus str. psy62]
          Length = 1187

 Score = 23.1 bits (48), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 1/67 (1%)

Query: 31  IFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTRIGSPSFFSTFARVEGME-GLADIS 89
           +  GD G GKT I    +F++   G + A  A  T +    F     R +G    +A IS
Sbjct: 650 LICGDVGFGKTEIALRAAFIAVMNGLQVAVIAPTTLLVRQHFRLFSERFQGFSVRIASIS 709

Query: 90  IKLETRD 96
             ++T++
Sbjct: 710 RFVQTKE 716


>gi|254780832|ref|YP_003065245.1| putative potassium uptake transport system protein [Candidatus
           Liberibacter asiaticus str. psy62]
          Length = 628

 Score = 23.1 bits (48), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 11/30 (36%), Positives = 18/30 (60%)

Query: 342 GSQIFMTGTDKSVFDSLNETAKFMRISNHQ 371
           G+ IF+T   ++V D+L +  K  RI + Q
Sbjct: 481 GTAIFLTSDSQAVPDALLQNIKHNRILHEQ 510


  Database: las_proteome
    Posted date:  Jun 5, 2011  6:30 PM
  Number of letters in database: 328,796
  Number of sequences in database:  1233
  
Lambda     K      H
   0.326    0.139    0.402 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 227,845
Number of Sequences: 1233
Number of extensions: 9375
Number of successful extensions: 58
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 34
Number of HSP's gapped (non-prelim): 27
length of query: 375
length of database: 328,796
effective HSP length: 75
effective length of query: 300
effective length of database: 236,321
effective search space: 70896300
effective search space used: 70896300
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 39 (19.6 bits)