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= 0001.0613.p
         (320 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309983|ref|YP_003774075.1| transmembrane protein [Herbaspi...   378   e-106
gi|300313191|ref|YP_003777283.1| transmembrane protein [Herbaspi...   282   2e-77

>gi|300309983|ref|YP_003774075.1| transmembrane protein
           [Herbaspirillum seropedicae SmR1]
          Length = 242

 Score =  378 bits (970), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 228/245 (93%), Positives = 234/245 (95%), Gaps = 3/245 (1%)

Query: 76  MWKGLLGGALLGLGLGALLSHFGLGGALASMISTILTVALIALAIMFVIRLVRRKSEGAQ 135
           MWKGLLGGALLGLGLGALLSHFGLGGALASMISTILTVALIALAIMFV+R+ RRKSE   
Sbjct: 1   MWKGLLGGALLGLGLGALLSHFGLGGALASMISTILTVALIALAIMFVVRMFRRKSE--- 57

Query: 136 ASQPAPAWASAAPQAADNASGTPQIGSLLKTDQSAAATTQGGFGGGFGNAEVAPAYGIPA 195
           ASQPAPAWA AAPQAADNAS TPQIGS+LKTDQSAAA TQGGFGGGFGNAE APAYG+PA
Sbjct: 58  ASQPAPAWAGAAPQAADNASATPQIGSMLKTDQSAAAATQGGFGGGFGNAEQAPAYGVPA 117

Query: 196 GFDTVGFVRNAKTYFIRLQAAWDKADINDIREFTTPEMFAELRLQIQERGTASNQTDVVS 255
           GFDTVGFVRNAKTYFIRLQAAWDKADINDIREFTTPEMFAELRLQIQERG ASNQTDVVS
Sbjct: 118 GFDTVGFVRNAKTYFIRLQAAWDKADINDIREFTTPEMFAELRLQIQERGAASNQTDVVS 177

Query: 256 LDAEVLGVETVGNDYLASVKFFGFIKEDPSASPAQFAEIWNLSKPATGQGGWVLAGIQQL 315
           LDAEVLGVETVGNDYLASVKFFGFIKEDP+ASPAQFAEIWNLSKPA GQGGWVLAGIQQ+
Sbjct: 178 LDAEVLGVETVGNDYLASVKFFGFIKEDPTASPAQFAEIWNLSKPAAGQGGWVLAGIQQI 237

Query: 316 DPVQA 320
           DPV A
Sbjct: 238 DPVSA 242


>gi|300313191|ref|YP_003777283.1| transmembrane protein
           [Herbaspirillum seropedicae SmR1]
          Length = 317

 Score =  282 bits (722), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 178/323 (55%), Positives = 222/323 (68%), Gaps = 14/323 (4%)

Query: 1   MKKAFVALIVAVMTLSVGMSAVEAKRLGGGGSIGKQSSSASRQA-QSPAPMQQNQAAAAK 59
           MKK  +AL++++ +LS+ MS  EAKRLGGGGS GKQSS+ SRQA  S     Q  A   +
Sbjct: 1   MKKLLLALLLSITSLSLIMSPAEAKRLGGGGSFGKQSSNYSRQAAPSSPSYSQPSATPYR 60

Query: 60  PAAPAA----APAAAAAKPSMWKGLLGGALLGLGLGALLSHFGLGGALASMISTILTVAL 115
           P+ PAA    AP    A P  W+ +LGGALLG GLGAL+SHFG+GGA+  ++ ++LT+AL
Sbjct: 61  PSTPAATLQSAPMPKPASP--WRNVLGGALLGFGLGALMSHFGIGGAMGGLLGSLLTIAL 118

Query: 116 IALAIMFVIRLVRRKSEGAQASQPAPAWASAAPQAA---DNASGTPQIGSLLKTDQSAAA 172
           +  A++F+IR+  R   G +A    PA+A+  P  +     A  TP+IGS L+ D +   
Sbjct: 119 LCAAVIFLIRMFAR---GREAQNNNPAYATPMPGVSPIGSAAGATPEIGSGLR-DINPPP 174

Query: 173 TTQGGFGGGFGNAEVAPAYGIPAGFDTVGFVRNAKTYFIRLQAAWDKADINDIREFTTPE 232
             QG   G          +GIP GFDT GFVRNAKTYFIRLQAAWD+AD+NDIREFTTPE
Sbjct: 175 ALQGNAYGAAAQPAQIQQWGIPEGFDTAGFVRNAKTYFIRLQAAWDRADVNDIREFTTPE 234

Query: 233 MFAELRLQIQERGTASNQTDVVSLDAEVLGVETVGNDYLASVKFFGFIKEDPSASPAQFA 292
           MFAELR+Q+ ERG A N TDVV LDA++LG+ET+  DYLA+V+F G IKE P  S   FA
Sbjct: 235 MFAELRMQLTERGAAPNATDVVQLDAQLLGIETMAFDYLATVRFQGLIKEAPDVSAEPFA 294

Query: 293 EIWNLSKPATGQGGWVLAGIQQL 315
           EIWNLSKP  G GGWVLAGIQQ+
Sbjct: 295 EIWNLSKPLNGSGGWVLAGIQQV 317


  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
   0.316    0.130    0.370 

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: 628,260
Number of extensions: 20837
Number of successful extensions: 68
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 64
Number of HSP's successfully gapped: 2
Length of query: 320
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 235
Effective length of database: 1,217,395
Effective search space: 286087825
Effective search space used: 286087825
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: 130 (54.7 bits)