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= 0001.0363.p
         (422 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309727|ref|YP_003773819.1| transmembrane protein [Herbaspi...   474   e-135

>gi|300309727|ref|YP_003773819.1| transmembrane protein
           [Herbaspirillum seropedicae SmR1]
          Length = 429

 Score =  474 bits (1219), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 274/441 (62%), Positives = 318/441 (72%), Gaps = 31/441 (7%)

Query: 1   MALATQCPHCLTIFRVASDQLKLRGGLVRCGSCREVFNGNEFLVEASIADGHYQPAPGSK 60
           MALATQCPHCLTIFRV SDQLKLRGGLVRCGSCR+VFNGN++LVEAS+ADGHYQPAPGSK
Sbjct: 1   MALATQCPHCLTIFRVVSDQLKLRGGLVRCGSCRQVFNGNDYLVEASVADGHYQPAPGSK 60

Query: 61  AQAGVARPAMRAAAAAAAAPAPAPASAPAASVPRA-APVASAPVLPDVRSQAAVPEVNAP 119
           AQAGV  P+  AA A          ++P A+  R  AP  SAPV        A+P  +  
Sbjct: 61  AQAGVMTPSAAAAPATPTPAPSPVPASPMAT--RGPAPQPSAPV-------HAIPVSSGT 111

Query: 120 APVAAKPAPVAPA-------IPVIAEPKVFRSPSSPGYIPDLGASLKPAEPVDKNKWDDD 172
           APV+A+P P           IPVIAEPKVFRSP+SPGYIPDLGA LK    VDK+K D+ 
Sbjct: 112 APVSAEPPPPVQVPAPVPAAIPVIAEPKVFRSPTSPGYIPDLGAPLKSPAAVDKDKRDEA 171

Query: 173 DPAAPPTLATSPDDAPDSGA-LLRRSSAEPEDVLAPPDVAAVF-----RIDDEPVLHEPP 226
           D   P  +A     AP  GA LLRRSS+  +++++  D+ A F     R+D+E V H   
Sbjct: 172 DALPPFPVADEIPTAPAGGAALLRRSSSTDDEIVSAADIDAAFGPATSRLDEEDVHH--- 228

Query: 227 LRRQE-----APAEESEEKFEDSDEAEEPGFVRRAQRKARISHMTKMVMMVLAGAMVPVL 281
           LR  E       A +     +  D+AE PGFVRR +R+ R   + K++MM+LAG MVPVL
Sbjct: 229 LRGHEDEPDQLSAADHSAADDSEDDAELPGFVRRVERRERAGRVLKVIMMILAGVMVPVL 288

Query: 282 LLQSLYYWRNPLAAAVPQLRPMLNGMCVSLHCTVGLPTEIERLSLEANELQVVPPSQNVY 341
           LLQ+LYYWRNPLA A+P +RPMLNGMCV+LHC+VGLP EI+RLSLEANELQVVPP+QNVY
Sbjct: 289 LLQALYYWRNPLAEALPPVRPMLNGMCVALHCSVGLPAEIDRLSLEANELQVVPPNQNVY 348

Query: 342 ALTVVMRNRSSTTQAWPDIELTLNNDDEKAVVRRVFRPRDYLADPTQADNGIGPESEQQI 401
           ALTVVMRNR    QAWP +ELTLNNDDEKAVVRRVFRPRDYL +  Q D GI  +SEQQI
Sbjct: 349 ALTVVMRNRGPGAQAWPHLELTLNNDDEKAVVRRVFRPRDYLPNARQIDRGIAADSEQQI 408

Query: 402 KLNFELKDALVSGYRVYLFYP 422
           KLNFELKDALVSGYRVYLFYP
Sbjct: 409 KLNFELKDALVSGYRVYLFYP 429


  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
   0.315    0.131    0.388 

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: 952,941
Number of extensions: 30190
Number of successful extensions: 113
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 109
Number of HSP's successfully gapped: 1
Length of query: 422
Length of database: 1,619,870
Length adjustment: 88
Effective length of query: 334
Effective length of database: 1,203,190
Effective search space: 401865460
Effective search space used: 401865460
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 (21.6 bits)
S2: 132 (55.5 bits)