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= 013554
         (441 letters)

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

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



>pdb|1O0W|A Chain A, Crystal Structure Of Ribonuclease Iii (Tm1102) From
           Thermotoga Maritima At 2.0 A Resolution
 pdb|1O0W|B Chain B, Crystal Structure Of Ribonuclease Iii (Tm1102) From
           Thermotoga Maritima At 2.0 A Resolution
          Length = 252

 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 41/138 (29%), Positives = 64/138 (46%), Gaps = 22/138 (15%)

Query: 163 DTLLYLAFQHP--FCERNKA-RHVRAGHSRLCFLGQFVLELAFCEFFLQRYP-------- 211
           + LL+ A  H     E+N+A R     + +L FLG  VLEL  CE   ++YP        
Sbjct: 35  EELLFRALCHSSYANEQNQAGRKDVESNEKLEFLGDAVLELFVCEILYKKYPEAEVGDLA 94

Query: 212 RESPAPMRERVFGLIGRR-NLPKWIKAASLQNLIFPFDEMDRLIRKEREPPVKSVFWALF 270
           R   A   E V  ++ R+ NL K+         +F     ++   ++R+  +   F AL 
Sbjct: 95  RVKSAAASEEVLAMVSRKMNLGKF---------LFLGKGEEKTGGRDRDSILADAFEALL 145

Query: 271 GAIYLCFGFPEVYRVLFE 288
            AIYL  G+ ++ + LFE
Sbjct: 146 AAIYLDQGYEKI-KELFE 162


>pdb|2A11|A Chain A, Crystal Structure Of Nuclease Domain Of Ribonuclase Iii
           From Mycobacterium Tuberculosis
          Length = 242

 Score = 39.3 bits (90), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 38/145 (26%), Positives = 55/145 (37%), Gaps = 11/145 (7%)

Query: 151 DQLGDDNPAKHFDTLLYLAFQH-PFCERNKARHVRAGHSRLCFLGQFVLELAFCEFFLQR 209
           D LG D P    D LL LA  H  +   N        + RL FLG  VL L   +    R
Sbjct: 12  DALGVDLP----DELLSLALTHRSYAYENGGLPT---NERLEFLGDAVLGLTITDALFHR 64

Query: 210 YPRESP---APMRERVFGLIGRRNLPKWIKAASLQNLIFPFDEMDRLIRKEREPPVKSVF 266
           +P  S    A +R  V       ++ + + A  L   +            ++   +    
Sbjct: 65  HPDRSEGDLAKLRASVVNTQALADVARRLCAEGLGVHVLLGRGEANTGGADKSSILADGM 124

Query: 267 WALFGAIYLCFGFPEVYRVLFEVFG 291
            +L GAIYL  G  +   V+  +FG
Sbjct: 125 ESLLGAIYLQHGMEKAREVILRLFG 149


>pdb|1V9K|A Chain A, The Crystal Structure Of The Catalytic Domain Of
           Pseudouridine Synthase Rluc From Escherichia Coli
 pdb|1V9K|B Chain B, The Crystal Structure Of The Catalytic Domain Of
           Pseudouridine Synthase Rluc From Escherichia Coli
          Length = 228

 Score = 31.6 bits (70), Expect = 0.89,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 369 MQTLGYPLVVQDRIPEITEARNI-ELGLGLQLCFLHPSKYKFEHP 412
            Q  G+P+   DR  +    R + E G GL   FLH +  KF HP
Sbjct: 157 TQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHP 201


>pdb|1XPI|A Chain A, Crystal Structure Of The Catalytic Domain Of E. Coli
           Pseudouridine Synthase Rluc
 pdb|1XPI|B Chain B, Crystal Structure Of The Catalytic Domain Of E. Coli
           Pseudouridine Synthase Rluc
          Length = 231

 Score = 31.6 bits (70), Expect = 0.97,   Method: Compositional matrix adjust.
 Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 1/44 (2%)

Query: 370 QTLGYPLVVQDRIPEITEARNI-ELGLGLQLCFLHPSKYKFEHP 412
           Q  G+P+   DR  +    R + E G GL   FLH +  KF HP
Sbjct: 161 QYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHP 204


>pdb|3BQ3|A Chain A, Crystal Structure Of S. Cerevisiae Dcn1
          Length = 270

 Score = 29.3 bits (64), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 18/80 (22%), Positives = 38/80 (47%), Gaps = 2/80 (2%)

Query: 298 ECQPKLRRQLEDVDYVSVEFEGNKLTWQDVAAYKPPEDALFAQPRLF-RACVPPGMHRFR 356
           +C PK+ R+    ++ ++ +  N    +++  +   E +  A P ++ +       H   
Sbjct: 27  KCDPKVSRKYLQRNHWNINYALNDYYDKEIGTF-TDEVSTVAHPPVYPKELTQVFEHYIN 85

Query: 357 GNLWDFDSRPQVMQTLGYPL 376
            NL+D DS  + ++ LGY L
Sbjct: 86  NNLFDIDSLVKFIEELGYNL 105


  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
   0.326    0.142    0.448 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,825,525
Number of Sequences: 62578
Number of extensions: 468861
Number of successful extensions: 1138
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1137
Number of HSP's gapped (non-prelim): 5
length of query: 441
length of database: 14,973,337
effective HSP length: 102
effective length of query: 339
effective length of database: 8,590,381
effective search space: 2912139159
effective search space used: 2912139159
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: 53 (25.0 bits)