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|254780237|ref|YP_003064650.1| DNA-directed RNA polymerase
subunit alpha [Candidatus Liberibacter asiaticus str. psy62]
         (340 letters)

Database: las_proteome 
           1233 sequences; 328,796 total letters

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



>gi|254780237|ref|YP_003064650.1| DNA-directed RNA polymerase subunit alpha [Candidatus Liberibacter
           asiaticus str. psy62]
          Length = 340

 Score =  696 bits (1796), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 340/340 (100%), Positives = 340/340 (100%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI
Sbjct: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ
Sbjct: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI
Sbjct: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE
Sbjct: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR
Sbjct: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
           KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC
Sbjct: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340


>gi|254780721|ref|YP_003065134.1| pilus component protein [Candidatus Liberibacter asiaticus str.
           psy62]
          Length = 329

 Score = 23.9 bits (50), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 8/66 (12%)

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           I+ ++  + V EDI  +S+P +       EE+ L++   + L    + +  +   RT+ D
Sbjct: 198 ISIDQALRRVAEDIGGQSVPLS-------EEMLLTIAELSFLPNRQVAF-ENFYNRTQMD 249

Query: 292 MLRMAN 297
            +R A 
Sbjct: 250 CVRNAT 255


>gi|254780170|ref|YP_003064583.1| cationic amino acid ABC transporter, periplasmic binding protein
           [Candidatus Liberibacter asiaticus str. psy62]
          Length = 342

 Score = 23.5 bits (49), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 9/36 (25%), Positives = 21/36 (58%), Gaps = 5/36 (13%)

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDL 284
           ++ ++P + ++VEE++ + R+  C       Y GD+
Sbjct: 168 NMKYHPIVFERVEEIDAAYRAHRC-----DAYTGDI 198


  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
   0.317    0.136    0.386 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 210,805
Number of Sequences: 1233
Number of extensions: 8694
Number of successful extensions: 23
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 21
Number of HSP's gapped (non-prelim): 4
length of query: 340
length of database: 328,796
effective HSP length: 75
effective length of query: 265
effective length of database: 236,321
effective search space: 62625065
effective search space used: 62625065
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 39 (19.6 bits)