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= 010589
         (506 letters)

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

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



>pdb|2XUT|A Chain A, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter.
 pdb|2XUT|B Chain B, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter.
 pdb|2XUT|C Chain C, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter
          Length = 524

 Score = 74.7 bits (182), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 84/370 (22%), Positives = 155/370 (41%), Gaps = 61/370 (16%)

Query: 53  IRPCVVAFAADQIDMRKATVANRKWNFFNWYYFCMGIATLTALTVVVYIQDNVGWGLGFG 112
           I+P V +F  DQ D    ++A +    F+ +YF +   +  A   +  +  N G  + FG
Sbjct: 126 IKPLVSSFMGDQFDQSNKSLAQKA---FDMFYFTINFGSFFASLSMPLLLKNFGAAVAFG 182

Query: 113 IPAIGMVMSVLAFVFGSPLYVKLKP------GGSPLTR---LTQV-----------IVAA 152
           IP + M ++ + F  G   Y+ + P      G  P+ R   LT+V           ++  
Sbjct: 183 IPGVLMFVATVFFWLGRKRYIHMPPEPKDPHGFLPVIRSALLTKVEGKGNIGLVLALIGG 242

Query: 153 FKKRKAIVPEDPRLLYRNGELDSVISVHGTLVHTNQFKWLDKAATVTEGETTNSSPPNLW 212
                A+V   P L    G   +++ V G +           A    + E    S P+  
Sbjct: 243 VSAAYALV-NIPTLGIVAGLCCAMVLVMGFV----------GAGASLQLERARKSHPD-- 289

Query: 213 RLATVHRVEELKSIIRMLPVWAAGILLVTASSHQHSFTIQQARTMNTHLTHSFKIPPASL 272
                  V+ ++S++R+L ++A      +    + S  I QA  M           PA +
Sbjct: 290 -----AAVDGVRSVLRILVLFALVTPFWSLFDQKASTWILQANDM----VKPQWFEPAMM 340

Query: 273 SIFGILTMLIGLALYERIFVPIARRFTGNPAGISCLQRMGVGFAINILATIVSSFVEIKR 332
                L +++ +     +  P   R       ++ L++MG G AI  L+ IV   +++  
Sbjct: 341 QALNPLLVMLLIPFNNFVLYPAIERMG---VKLTALRKMGAGIAITGLSWIVVGTIQL-- 395

Query: 333 KKVAANHHLLDDPKAIIPISVFWLVPQYCLHGVAEVFMSVGHLEFLYDQSPESMRSTAVA 392
                   ++D   A+   S+FW +  Y L    EV +S   LEF Y Q+P++M+ T ++
Sbjct: 396 --------MMDGGSAL---SIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAMKGTIMS 444

Query: 393 LYWIAISMGN 402
            + +++++GN
Sbjct: 445 FWTLSVTVGN 454


>pdb|1W36|B Chain B, Recbcd:dna Complex
 pdb|1W36|E Chain E, Recbcd:dna Complex
 pdb|3K70|B Chain B, Crystal Structure Of The Complete Initiation Complex Of
           Recbcd
 pdb|3K70|E Chain E, Crystal Structure Of The Complete Initiation Complex Of
           Recbcd
          Length = 1180

 Score = 30.4 bits (67), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 4/44 (9%)

Query: 171 GELDSVISVHG----TLVHTNQFKWLDKAATVTEGETTNSSPPN 210
           GELD++I   G        +NQ KW+DK +   E ET +   P 
Sbjct: 241 GELDALIESSGIDRRKFNRSNQAKWIDKISAWAEEETNSYQLPE 284


>pdb|3QYB|A Chain A, X-Ray Crystal Structure Of Human Tbc1d4 (As160) Rabgap
           Domain
          Length = 301

 Score = 29.6 bits (65), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 14/41 (34%), Positives = 22/41 (53%)

Query: 238 LLVTASSHQHSFTIQQARTMNTHLTHSFKIPPASLSIFGIL 278
           LL   ++ QH+  +   RT  TH   S ++ P  LS+F +L
Sbjct: 86  LLKQLTAQQHAILVDLGRTFPTHPYFSVQLGPGQLSLFNLL 126


  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
   0.325    0.139    0.433 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,840,719
Number of Sequences: 62578
Number of extensions: 522861
Number of successful extensions: 1231
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1224
Number of HSP's gapped (non-prelim): 9
length of query: 506
length of database: 14,973,337
effective HSP length: 103
effective length of query: 403
effective length of database: 8,527,803
effective search space: 3436704609
effective search space used: 3436704609
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 bits)