BLASTP 2.2.26 [Sep-21-2011]


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= 018408
         (356 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

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



>pdb|4GBY|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To D-Xylose
 pdb|4GBZ|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To D-Glucose
 pdb|4GC0|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To
           6-Bromo-6-Deoxy-D-Glucose
          Length = 491

 Score = 75.9 bits (185), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 58/247 (23%), Positives = 105/247 (42%), Gaps = 31/247 (12%)

Query: 86  FPHVLIASMSNFLFGYHIGVMNGPIVSIA------KELGFEGNPILEGLVVSIFIAGAFV 139
           F   L+A++   LFGY   V++G + S+       + L       L G  V+  + G  +
Sbjct: 11  FSITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVASALIGCII 70

Query: 140 GSISSGSLADKLGCRRTFQIDTIPLILGAIISAQ------------------AHSLDEML 181
           G    G  +++ G R + +I  +   +  + SA                   A  + E +
Sbjct: 71  GGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGYVPEFV 130

Query: 182 WGRFLVGLGIGVNTVLVPIYISEVAPTKYRGSLGTLCQVGTCLG--IITSLFLGIPAEDD 239
             R + G+G+G+ ++L P+YI+E+AP   RG L +  Q     G  ++  +   I    D
Sbjct: 131 IYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGD 190

Query: 240 PHW-----WRTMLYIASLPGFILALGMQFTVESPRWLCKGGMLNDAKAVIANLWGESEIN 294
             W     WR M     +P  +  + +    ESPRWL   G    A+ ++  + G +   
Sbjct: 191 ASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGNTLAT 250

Query: 295 KAIEEFQ 301
           +A++E +
Sbjct: 251 QAVQEIK 257


>pdb|4DEX|A Chain A, Crystal Structure Of The Voltage Dependent Calcium Channel
           Beta-2 Subunit In Complex With The Cav2.2 I-Ii Linker
          Length = 339

 Score = 32.7 bits (73), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 11/32 (34%), Positives = 21/32 (65%)

Query: 22  FTPSPAKMKTLRFSFSHRSTKFKVLAAKKQLP 53
           F PSP K++ +R     R+ +FK+ + +K++P
Sbjct: 96  FIPSPVKLENMRLQHEQRAKEFKLHSKEKRMP 127


>pdb|4DEY|A Chain A, Crystal Structure Of The Voltage Dependent Calcium Channel
           Beta-2 Subunit In Complex With The Cav1.2 I-Ii Linker
          Length = 337

 Score = 32.3 bits (72), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 11/32 (34%), Positives = 21/32 (65%)

Query: 22  FTPSPAKMKTLRFSFSHRSTKFKVLAAKKQLP 53
           F PSP K++ +R     R+ +FK+ + +K++P
Sbjct: 94  FIPSPVKLENMRLQHEQRAKEFKLHSKEKRMP 125


>pdb|2WW8|A Chain A, Structure Of The Pilus Adhesin (Rrga) From Streptococcus
           Pneumoniae
          Length = 893

 Score = 30.4 bits (67), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 21/86 (24%), Positives = 42/86 (48%), Gaps = 5/86 (5%)

Query: 262 QFTVE---SPRWLCKGGMLNDAKAVIANLWGESEINKAIEEFQLVIKKDGSDLDSQWSEL 318
           Q+TVE   + R   +G  + + +  +++ + ++     ++    +IK DGS+ + Q   L
Sbjct: 116 QWTVEVEKNGRTTVQGEQVENREEALSDQYPQTGTYPDVQTPYQIIKVDGSEKNGQHKAL 175

Query: 319 LEEPHSRVAFIGDGALASLLVGVTNF 344
              P+ RV  I +G L+  +  V N 
Sbjct: 176 NPNPYERV--IPEGTLSKRIYQVNNL 199


>pdb|4IXN|A Chain A, Crystal Structure Of Zn(ii)-bound E37a,c66a,c67a Triple
           Mutant Yjia Gtpase
 pdb|4IXN|B Chain B, Crystal Structure Of Zn(ii)-bound E37a,c66a,c67a Triple
           Mutant Yjia Gtpase
          Length = 318

 Score = 28.5 bits (62), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 4/44 (9%)

Query: 287 LWGESEINKAIEEFQLVIKKDGSDLDSQWSELLEEPHSRVAFIG 330
           LW + E N+ +  FQ V +   +D D  W +  E+PHS + FIG
Sbjct: 262 LWIDGEPNRLL--FQGVQRLYSADWDRPWGD--EKPHSTMVFIG 301


>pdb|1NIJ|A Chain A, Yjia Protein
 pdb|4IXM|A Chain A, Crystal Structure Of Zn(ii)-bound Yjia Gtpase From E. Coli
 pdb|4IXM|B Chain B, Crystal Structure Of Zn(ii)-bound Yjia Gtpase From E. Coli
          Length = 318

 Score = 28.5 bits (62), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 4/44 (9%)

Query: 287 LWGESEINKAIEEFQLVIKKDGSDLDSQWSELLEEPHSRVAFIG 330
           LW + E N+ +  FQ V +   +D D  W +  E+PHS + FIG
Sbjct: 262 LWIDGEPNRLL--FQGVQRLYSADWDRPWGD--EKPHSTMVFIG 301


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.322    0.139    0.424 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,450,499
Number of Sequences: 62578
Number of extensions: 425700
Number of successful extensions: 827
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 822
Number of HSP's gapped (non-prelim): 10
length of query: 356
length of database: 14,973,337
effective HSP length: 100
effective length of query: 256
effective length of database: 8,715,537
effective search space: 2231177472
effective search space used: 2231177472
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)