BLASTP 2.2.18 [Mar-02-2008]


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= 0002.0041.p
         (271 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309718|ref|YP_003773810.1| ABC transporter permease [Herba...   425   e-120
gi|300309497|ref|YP_003773589.1| ABC transporter permease [Herba...    60   2e-10

>gi|300309718|ref|YP_003773810.1| ABC transporter permease
           [Herbaspirillum seropedicae SmR1]
          Length = 270

 Score =  425 bits (1092), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 231/270 (85%), Positives = 252/270 (93%), Gaps = 1/270 (0%)

Query: 1   MQTYFFILAALLYLGCAFLPSERRLPISLGTVIGWLLHGGALVYDMFAPDAVRVGFAVML 60
           MQTYFFILAALLYL CAF+PS+RR+PISLG V GW+LHGGAL+ DMFAPDA+RVGFAVML
Sbjct: 1   MQTYFFILAALLYLACAFMPSQRRMPISLGIVAGWVLHGGALLSDMFAPDALRVGFAVML 60

Query: 61  SATMWVSVAAYWLENRNFSLDSLRVLVLPVAAVAVILPSVFPGNMVELAGKSDWFLWHIA 120
           S+T+W+SVAAYWLENRNFSLDS+RVLVLPVAA+AV+LPS+FPGNMV L GKSDWFL HIA
Sbjct: 61  SSTLWISVAAYWLENRNFSLDSMRVLVLPVAALAVVLPSIFPGNMVALTGKSDWFLAHIA 120

Query: 121 VSILAYSTLTIAAFHAVLMVLQESRLHTRPKMGAAQPGWFSIALDRLPALLTMEKILFRL 180
           +SILAYSTLTIAAFHAVLMVLQESRLHTRP + A Q GWF +ALDRLPALLTMEK+LFRL
Sbjct: 121 ISILAYSTLTIAAFHAVLMVLQESRLHTRPGL-ATQSGWFGLALDRLPALLTMEKLLFRL 179

Query: 181 IAFGFVLLTLTVLSGVVFSEQLFQKAFRWDHKTIFTLLSWCLFGLLLAGRKWQGWRGRTA 240
           IAFGF LLTLTVLSGVVFSEQLF    +WDHKTIFT+LSW LFGLLLAGR+WQGWRGRTA
Sbjct: 180 IAFGFTLLTLTVLSGVVFSEQLFGTPLKWDHKTIFTMLSWLLFGLLLAGRRWQGWRGRTA 239

Query: 241 LSFTLAGFAILLLAYVGSRFVLEVVLHRIL 270
           LSFTLAGFAILLLAYVGSRFVLEVVLHR+L
Sbjct: 240 LSFTLAGFAILLLAYVGSRFVLEVVLHRVL 269


>gi|300309497|ref|YP_003773589.1| ABC transporter permease
           [Herbaspirillum seropedicae SmR1]
          Length = 384

 Score = 59.7 bits (143), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 47/184 (25%), Positives = 85/184 (46%), Gaps = 21/184 (11%)

Query: 85  VLVLPVAAVAVILPSVFPGNMVEL-----AGKSDWFLWHIAVSILAYSTLTIAAFHAVLM 139
           VL +  AAVA ++      +  E+     A +S W   H+  + + Y T  +AA  AV  
Sbjct: 209 VLTVITAAVAFLMWYTVSRDAAEIQPLVPALQSWWMKIHVPANFIGYGTFALAAMVAVAY 268

Query: 140 VLQESRLHTRPKMGAAQPGWFSIALDRLPALLTMEKILFRLIAFGFVLLTLTVLSGVVFS 199
           +L+             Q G+ +   DRLP+L  ++ ++++ IA GF   T+  + G +++
Sbjct: 269 LLR-------------QKGYLA---DRLPSLEVLDDVMYKAIAVGFAFFTIATILGALWA 312

Query: 200 EQLFQKAFRWDHKTIFTLLSWCLFGLLLAGRKWQGWRGRTALSFTLAGFAILLLAYVGSR 259
            + +   + WD K  + L+ W  +   L  R  +G RG+ A  + L G  +   A++G  
Sbjct: 313 AEAWGGYWSWDPKETWALIVWLNYAAWLHMRLMKGLRGQAAAWWALVGLLVTTFAFLGVN 372

Query: 260 FVLE 263
             L 
Sbjct: 373 MFLS 376


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.332    0.142    0.454 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 754,626
Number of extensions: 26648
Number of successful extensions: 104
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 102
Number of HSP's successfully gapped: 2
Length of query: 271
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 187
Effective length of database: 1,222,130
Effective search space: 228538310
Effective search space used: 228538310
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 130 (54.7 bits)