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= 0001.4049.p
         (188 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313467|ref|YP_003777559.1| type IV pilus biogenesis protei...    56   2e-09

>gi|300313467|ref|YP_003777559.1| type IV pilus biogenesis protein
           [Herbaspirillum seropedicae SmR1]
          Length = 186

 Score = 56.2 bits (134), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 93/190 (48%), Positives = 117/190 (61%), Gaps = 14/190 (7%)

Query: 1   MSCGFDFSCSPAQRRRIRERNFYRALSAAVLLGCLLALLPGARIFLHTRSFQEANALLRQ 60
           M+   DF+  PA RRR RE+ F+  L AA LLG LLA+ PG RI LH      ANALL Q
Sbjct: 1   MNSVIDFAHPPALRRRRREQRFHGWLCAAALLGVLLAMAPGLRIHLHQGRLAAANALLLQ 60

Query: 61  ALHSLAPQVQQTAALRQRIEALEKQLAAQQQLTLRRQQASLLLRSAAQAAQAANSPL-RL 119
              +LA   +Q A L+ RI AL+++LA QQQL  RR QA LLLR  A+    A+ PL  L
Sbjct: 61  EAQALASATRQAAELQTRISALQQRLAQQQQLARRRTQAGLLLRGVAR----ASLPLVHL 116

Query: 120 QRILLQADRAELRGQAASAQELRDFTNALASAGLEGATLNDLQAEDGA----YAFSLIIP 175
           +R+ LQ D AELRG+A S   +++   ALA+AGLEGA L DL+ +  A    Y++SL IP
Sbjct: 117 ERLTLQKDHAELRGRAGSMAAIQELQGALAAAGLEGAHLLDLRTQASAAAEGYSWSLSIP 176

Query: 176 L-----APPP 180
           L     A PP
Sbjct: 177 LLAAGAASPP 186


  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
   0.322    0.131    0.361 

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: 362,891
Number of extensions: 9127
Number of successful extensions: 92
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 91
Number of HSP's successfully gapped: 1
Length of query: 188
Length of database: 1,619,870
Length adjustment: 80
Effective length of query: 108
Effective length of database: 1,241,070
Effective search space: 134035560
Effective search space used: 134035560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 128 (53.9 bits)