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= 0001.3976.p
         (252 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313397|ref|YP_003777489.1| LamB/YcsF family protein [Herba...   469   e-133
gi|300311089|ref|YP_003775181.1| LamB/YcsF family protein [Herba...   172   4e-44

>gi|300313397|ref|YP_003777489.1| LamB/YcsF family protein
           [Herbaspirillum seropedicae SmR1]
          Length = 252

 Score =  469 bits (1206), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 229/252 (90%), Positives = 239/252 (94%)

Query: 1   MRKIDLNSDMGEGFGPWTIGDGVDEAIMPLISSANIATGFHAGDPNIMRRTVEQARRHGV 60
           M+ +DLNSDMGEGFGPWTIGDGVD AI+PLISSANIATGFHAGDPN MRRTVE AR+HGV
Sbjct: 1   MKTVDLNSDMGEGFGPWTIGDGVDAAILPLISSANIATGFHAGDPNTMRRTVELARQHGV 60

Query: 61  AIGAHPGFRDLVGFGRRHLNAPATELVNDMLYQLGALREFARLNGMNLQHIKPHGALYMH 120
           AIGAHPGFRDLVGFGRRHLNAPA ELVNDMLYQLGALREFARLNG+ LQHIKPHGALYMH
Sbjct: 61  AIGAHPGFRDLVGFGRRHLNAPAIELVNDMLYQLGALREFARLNGLPLQHIKPHGALYMH 120

Query: 121 LARDEEAARVFVQTLRQLDSNLLLFCMNGSAIWRVAQELGQAVVCEFYADRDYDHSGSIV 180
           LARDEEAARVFVQTLRQLD NLLLFCM+GSA+WRVAQEL QAVVCEFYADRDYD+SGSIV
Sbjct: 121 LARDEEAARVFVQTLRQLDPNLLLFCMHGSAVWRVAQELQQAVVCEFYADRDYDNSGSIV 180

Query: 181 FTRRVGALDPDQVAAKVLRACREGVVRTVEGQDIPIRFDSVCIHSDTPGALALVQATRAS 240
           FTRRVGALD  QVAAKVLRAC EGVVRTVEG+DIPI FDSVCIHSDTPGALALVQATR S
Sbjct: 181 FTRRVGALDAAQVAAKVLRACCEGVVRTVEGRDIPIAFDSVCIHSDTPGALALVQATRNS 240

Query: 241 LEAADIAVAAPR 252
           LEAADIA+AAPR
Sbjct: 241 LEAADIAIAAPR 252


>gi|300311089|ref|YP_003775181.1| LamB/YcsF family protein
           [Herbaspirillum seropedicae SmR1]
          Length = 246

 Score =  172 bits (435), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 101/250 (40%), Positives = 138/250 (55%), Gaps = 11/250 (4%)

Query: 4   IDLNSDMGEGFGPWTIGDGVDEAIMPLISSANIATGFHAGDPNIMRRTVEQARRHGVAIG 63
           IDLN+D+GEG          DE ++ L+SSANIA G+HAGD N MRR+V  A ++ VAIG
Sbjct: 3   IDLNADLGEGCD-------TDEQLLTLVSSANIACGWHAGDANTMRRSVRWAIQNHVAIG 55

Query: 64  AHPGFRDLVGFGRRHLNAPATELVNDMLYQLGALREFARLNGMNLQHIKPHGALYMHLAR 123
           AHP F D   FGR  +  P  E+V+ MLYQLGAL    R  G  + H+KPHGALY   A+
Sbjct: 56  AHPSFPDRENFGRSAMQLPPEEIVSGMLYQLGALEAIVRAEGGRMTHVKPHGALYNQAAK 115

Query: 124 DEEAARVFVQTLRQLDSNLLLFCMNGSAIWRVAQELGQAVVCEFYADRDYDHSGSIVFTR 183
           D   A      +R  +  L L+ + GS +   A+      V E +ADR Y+  GS+V   
Sbjct: 116 DAVLANAICAAIRTFNPELSLYGLAGSELIAAARHADLNAVEEVFADRAYEADGSLVARS 175

Query: 184 RVGAL---DPDQVAAKVLRACREGVVRTVEGQDIPIRFDSVCIHSDTPGALALVQATRAS 240
           + GAL   D D + A+ L   ++  V+ ++G  + +   +VC+H D   AL   +  RA 
Sbjct: 176 KPGALIDNDADAI-AQTLMLVKQKKVKAIDGSIVEVNAQTVCLHGDGAHALDFARQIRAR 234

Query: 241 LEAADIAVAA 250
           L    IAV A
Sbjct: 235 LHEERIAVRA 244


  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
   0.324    0.138    0.415 

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: 838,830
Number of extensions: 36402
Number of successful extensions: 154
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 152
Number of HSP's successfully gapped: 2
Length of query: 252
Length of database: 1,619,870
Length adjustment: 83
Effective length of query: 169
Effective length of database: 1,226,865
Effective search space: 207340185
Effective search space used: 207340185
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 129 (54.3 bits)