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= 004516
         (747 letters)

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

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



>pdb|1G8A|A Chain A, Pyrococcus Horikoshii Fibrillarin Pre-Rrna Processing
           Protein
          Length = 227

 Score = 29.3 bits (64), Expect = 8.5,   Method: Composition-based stats.
 Identities = 17/44 (38%), Positives = 27/44 (61%), Gaps = 3/44 (6%)

Query: 289 KQQKKYFDDVELKKRELNEIGKYIEELNQDPASKDKELKFVQQS 332
           K+ ++ F +VE   REL+E  + IE LN +P  KD  L  V+++
Sbjct: 187 KEPEQVFREVE---RELSEYFEVIERLNLEPYEKDHALFVVRKT 227


>pdb|3DO6|A Chain A, Crystal Structure Of Putative Formyltetrahydrofolate
           Synthetase (Tm1766) From Thermotoga Maritima At 1.85 A
           Resolution
 pdb|3DO6|B Chain B, Crystal Structure Of Putative Formyltetrahydrofolate
           Synthetase (Tm1766) From Thermotoga Maritima At 1.85 A
           Resolution
          Length = 543

 Score = 29.3 bits (64), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 25/100 (25%), Positives = 46/100 (46%), Gaps = 22/100 (22%)

Query: 272 LHENEVESLEQELDSMRKQQKKYFDDVELKKRELNEIGKYIEELNQDPASKDKELKFVQQ 331
           +HE  +E+L++   ++R   +       L+K  L      +  LN+     +KE+ +V  
Sbjct: 334 IHEENLEALKEGFKNLRVHVEN------LRKFNL----PVVVALNRFSTDTEKEIAYV-- 381

Query: 332 SIKEC---------SKEFQWKKEESISTEKTIAECSKEVE 362
            +KEC         S+ F+   E  +   K +AE +K+VE
Sbjct: 382 -VKECEKLGVRVAVSEVFKKGSEGGVELAKAVAEAAKDVE 420


>pdb|2NNW|B Chain B, Alternative Conformations Of Nop56/58-fibrillarin Complex
           And Implication For Induced-fit Assenly Of Box C/d Rnps
 pdb|2NNW|D Chain D, Alternative Conformations Of Nop56/58-fibrillarin Complex
           And Implication For Induced-fit Assenly Of Box C/d Rnps
 pdb|3NMU|F Chain F, Crystal Structure Of Substrate-Bound Halfmer Box CD RNP
 pdb|3NMU|J Chain J, Crystal Structure Of Substrate-Bound Halfmer Box CD RNP
 pdb|3NVK|I Chain I, Structural Basis For Substrate Placement By An Archaeal
           Box CD Ribonucleoprotein Particle
 pdb|3NVK|J Chain J, Structural Basis For Substrate Placement By An Archaeal
           Box CD Ribonucleoprotein Particle
 pdb|3NVM|B Chain B, Structural Basis For Substrate Placement By An Archaeal
           Box CD Ribonucleoprotein Particle
          Length = 234

 Score = 28.9 bits (63), Expect = 9.6,   Method: Composition-based stats.
 Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 3/43 (6%)

Query: 289 KQQKKYFDDVELKKRELNEIGKYIEELNQDPASKDKELKFVQQ 331
           K+ ++ F +VE   REL+E  + IE LN +P  KD  L  V++
Sbjct: 194 KEPEQVFKEVE---RELSEYFEVIERLNLEPYEKDHALFVVRK 233


  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
   0.314    0.130    0.362 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,862,168
Number of Sequences: 62578
Number of extensions: 709443
Number of successful extensions: 2162
Number of sequences better than 100.0: 65
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 48
Number of HSP's that attempted gapping in prelim test: 2061
Number of HSP's gapped (non-prelim): 126
length of query: 747
length of database: 14,973,337
effective HSP length: 106
effective length of query: 641
effective length of database: 8,340,069
effective search space: 5345984229
effective search space used: 5345984229
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 55 (25.8 bits)