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= 039808
         (358 letters)

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

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



>pdb|3T6Q|A Chain A, Crystal Structure Of Mouse Rp105MD-1 Complex
 pdb|3T6Q|B Chain B, Crystal Structure Of Mouse Rp105MD-1 Complex
          Length = 606

 Score = 32.7 bits (73), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 43/166 (25%), Positives = 66/166 (39%), Gaps = 17/166 (10%)

Query: 181 GKELTTVIFPSLENLSIHHLW--NLTHICEGSVPNGSFARLRILSVHACPKLKFVF---S 235
           G +   VIF  L+N +I  LW      + +  +    F  L  +SV +    K  F   S
Sbjct: 211 GTQNLLVIFKGLKNSTIQSLWLGTFEDMDDEDISPAVFEGLCEMSVESINLQKHYFFNIS 270

Query: 236 SFMIHFMSNLEDLTVEDCPAXXXXXXXXXXXDSGCTALPRLKKLTL--HYLPGLVTIWSS 293
           S   H  S L++L +                 SG   L  LKKL L  +    L  I +S
Sbjct: 271 SNTFHCFSGLQELDL--------TATHLSELPSGLVGLSTLKKLVLSANKFENLCQISAS 322

Query: 294 AWPSLEYVSFYDCPRLKNIGLGSNLKHSVMEIKAEKSWWDDLEWED 339
            +PSL ++S       K + LG+    ++  ++      DD+E  D
Sbjct: 323 NFPSLTHLSIKG--NTKRLELGTGCLENLENLRELDLSHDDIETSD 366


>pdb|3E35|A Chain A, Actinobacteria-Specific Protein Of Unknown Function,
           Sco1997
          Length = 325

 Score = 31.6 bits (70), Expect = 0.74,   Method: Compositional matrix adjust.
 Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 15/68 (22%)

Query: 75  FLQRCVAWNAQCLTEFRIV-VGHDIKNIVSRVPDAVAFDYNKQGKCLRFINGENIPDAVL 133
           F +  V  +A+ L E+R+   GHD+  + + VP               ++     PDA L
Sbjct: 173 FEEAQVPGSAEALVEYRLAQAGHDVLGVAAHVP--------------HYVARSAYPDAAL 218

Query: 134 QILACCTA 141
            +L   TA
Sbjct: 219 TVLEAITA 226


>pdb|3TO5|A Chain A, High Resolution Structure Of Chey3 From Vibrio Cholerae
          Length = 134

 Score = 30.8 bits (68), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 27/89 (30%), Positives = 39/89 (43%), Gaps = 11/89 (12%)

Query: 267 DSGCTALPRLKKLTLHYLPGLVTIWSSAWPSLEYVSFYDCPRLKNIGLGSNLKH-SVMEI 325
           D G TALP LKK    +   +VT W+   P ++ +       LKNI     LKH  V+ I
Sbjct: 44  DDGLTALPMLKKGDFDF---VVTDWN--MPGMQGIDL-----LKNIRADEELKHLPVLMI 93

Query: 326 KAEKSWWDDLEWEDTELQLHLQNCFTTIS 354
            AE      +E     +  ++   FT  +
Sbjct: 94  TAEAKREQIIEAAQAGVNGYIVKPFTAAT 122


>pdb|2JGP|A Chain A, Structure Of The Tycc5-6 Pcp-C Bidomain Of The Tyrocidine
           Synthetase Tycc
          Length = 520

 Score = 29.6 bits (65), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 23/88 (26%), Positives = 39/88 (44%), Gaps = 11/88 (12%)

Query: 35  VYPGDKRWYKDVKSVV--LEVCNLTELSSLCFHFPEIKLLELFL---------QRCVAWN 83
           + P  K+ Y  V S    + + +  E   + ++ P   L+E  L         QR +A +
Sbjct: 88  IEPVQKQAYYPVSSAQKRMYILDQFEGVGISYNMPSTMLIEGKLERTRVEAAFQRLIARH 147

Query: 84  AQCLTEFRIVVGHDIKNIVSRVPDAVAF 111
               T F +V G  ++NI   VP A+A+
Sbjct: 148 ESLRTSFAVVNGEPVQNIHEDVPFALAY 175


>pdb|1ZXZ|A Chain A, X-Ray Structure Of Peptide Deformylase From Arabidopsis
           Thaliana (Atpdf1a); Crystals Grown In Peg-5000 Mme As
           Precipitant
 pdb|1ZXZ|B Chain B, X-Ray Structure Of Peptide Deformylase From Arabidopsis
           Thaliana (Atpdf1a); Crystals Grown In Peg-5000 Mme As
           Precipitant
 pdb|1ZY0|A Chain A, X-Ray Structure Of Peptide Deformylase From Arabidopsis
           Thaliana (Atpdf1a); Crystals Grown In Peg-6000
 pdb|1ZY0|B Chain B, X-Ray Structure Of Peptide Deformylase From Arabidopsis
           Thaliana (Atpdf1a); Crystals Grown In Peg-6000
 pdb|1ZY1|A Chain A, X-Ray Structure Of Peptide Deformylase From Arabidopsis
           Thaliana (Atpdf1a) In Complex With Met-Ala-Ser
 pdb|1ZY1|B Chain B, X-Ray Structure Of Peptide Deformylase From Arabidopsis
           Thaliana (Atpdf1a) In Complex With Met-Ala-Ser
          Length = 197

 Score = 28.1 bits (61), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 5/77 (6%)

Query: 99  KNIVSRVPDAVAFDYNKQGKCLRFINGENIPDAVLQILACCTAFYLDNHLHINSLSDFGV 158
           +  V R  + V   Y++QGK +  +N       +LQ    C   +LD +L+++ +     
Sbjct: 118 RAAVERYLEVVVTGYDRQGKRIE-VNASGWQARILQ--HECD--HLDGNLYVDKMVPRTF 172

Query: 159 RSINGLKFCIISECPKI 175
           R+++ L   +   CPK+
Sbjct: 173 RTVDNLDLPLAEGCPKL 189


  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
   0.324    0.139    0.444 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,579,746
Number of Sequences: 62578
Number of extensions: 408297
Number of successful extensions: 1273
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1272
Number of HSP's gapped (non-prelim): 6
length of query: 358
length of database: 14,973,337
effective HSP length: 100
effective length of query: 258
effective length of database: 8,715,537
effective search space: 2248608546
effective search space used: 2248608546
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 52 (24.6 bits)