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= 035716
         (308 letters)

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

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



>pdb|3M66|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
           Termination Factor 3
          Length = 270

 Score = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 54/238 (22%), Positives = 101/238 (42%), Gaps = 42/238 (17%)

Query: 43  SLLQNHPLYPPTQANLSFQ--IKEKILCLEIMGVDS---GKALSLNPSLHSASLNSIEGI 97
           S ++ HP        L F+  IK+ +L L+ +G++    G  L+ N ++ S  L +++  
Sbjct: 20  SKIEKHPEAANLLLRLDFEKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLENLKTR 79

Query: 98  ISFLQSKGILQKDLPRIFGMCPKVLTANIKTDLEPVFNFLSHDLEVPEHDFRKVINKCPR 157
           +++L SK   + D+ ++    P +L  +++  L+    F   +LE+     R ++ + PR
Sbjct: 80  VAYLHSKNFSKADVAQMVRKAPFLLNFSVER-LDNRLGFFQKELELSVKKTRDLVVRLPR 138

Query: 158 LLTSSARDQLKPALFYLQRLGFKDLNALAYQDSVLLVSKVENTLIPKLKYLESIGFSKDE 217
           LLT S    L+P                            EN  + +L+    +GF  +E
Sbjct: 139 LLTGS----LEPV--------------------------KENMKVYRLE----LGFKHNE 164

Query: 218 AVLMVLRCPGLFTFSIENNFKPKFEYFNXXXXXXXXXXXXFPQYFAFSLEKRIKPRHM 275
              M+ R P + T + +      F++ +            FPQ F   L K +K RH+
Sbjct: 165 IQHMITRIPKMLTAN-KMKLTETFDFVHNVMSIPHHIIVKFPQVFNTRLFK-VKERHL 220


>pdb|3OPG|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
           Termination Factor 3
          Length = 298

 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 54/238 (22%), Positives = 101/238 (42%), Gaps = 42/238 (17%)

Query: 43  SLLQNHPLYPPTQANLSFQ--IKEKILCLEIMGVDS---GKALSLNPSLHSASLNSIEGI 97
           S ++ HP        L F+  IK+ +L L+ +G++    G  L+ N ++ S  L +++  
Sbjct: 48  SKIEKHPEAANLLLRLDFEKDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLENLKTR 107

Query: 98  ISFLQSKGILQKDLPRIFGMCPKVLTANIKTDLEPVFNFLSHDLEVPEHDFRKVINKCPR 157
           +++L SK   + D+ ++    P +L  +++  L+    F   +LE+     R ++ + PR
Sbjct: 108 VAYLHSKNFSKADVAQMVRKAPFLLNFSVER-LDNRLGFFQKELELSVKKTRDLVVRLPR 166

Query: 158 LLTSSARDQLKPALFYLQRLGFKDLNALAYQDSVLLVSKVENTLIPKLKYLESIGFSKDE 217
           LLT S    L+P                            EN  + +L+    +GF  +E
Sbjct: 167 LLTGS----LEPV--------------------------KENMKVYRLE----LGFKHNE 192

Query: 218 AVLMVLRCPGLFTFSIENNFKPKFEYFNXXXXXXXXXXXXFPQYFAFSLEKRIKPRHM 275
              M+ R P + T + +      F++ +            FPQ F   L K +K RH+
Sbjct: 193 IQHMITRIPKMLTAN-KMKLTETFDFVHNVMSIPHHIIVKFPQVFNTRLFK-VKERHL 248


>pdb|4FZV|B Chain B, Crystal Structure Of The Human Mterf4:nsun4:sam Ternary
           Complex
          Length = 239

 Score = 30.4 bits (67), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 30/135 (22%), Positives = 55/135 (40%), Gaps = 7/135 (5%)

Query: 79  ALSLNPSLHSASLNSIEGIISFLQSKGILQKDLPRIFGMCPKVLTANIKTDLEPVFNFLS 138
            L  +P L    +  +    S+LQ  G+ +  L R+   CP++ T   + D+      L 
Sbjct: 53  VLKKSPQLLKLPIMQMRKRSSYLQKLGLGEGKLKRVLYCCPEIFTMR-QQDINDTVRLLK 111

Query: 139 HDLEVPEHDFRKVINKCPRLLTSSARDQLKPALFYLQ-RLGFKDLNALAYQDSVLLVSKV 197
                      K+++ CP +L      QL+    Y   R+G K  + +  +     ++K+
Sbjct: 112 EKCLFTVQQVTKILHSCPSVLREDL-GQLEYKFQYAYFRMGIKHPDIVKSEYLQYSLTKI 170

Query: 198 ENTLIPKLKYLESIG 212
           +   I    YLE +G
Sbjct: 171 KQRHI----YLERLG 181


>pdb|4FP9|B Chain B, Human Mterf4-Nsun4 Protein Complex
 pdb|4FP9|E Chain E, Human Mterf4-Nsun4 Protein Complex
 pdb|4FP9|G Chain G, Human Mterf4-Nsun4 Protein Complex
 pdb|4FP9|H Chain H, Human Mterf4-Nsun4 Protein Complex
          Length = 335

 Score = 30.0 bits (66), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 27/118 (22%), Positives = 50/118 (42%), Gaps = 13/118 (11%)

Query: 99  SFLQSKGILQKDLPRIFGMCPKVLTANIKTDLEPVFNFLSHDLEVPEHDFRKVINKCPRL 158
           S+LQ  G+ +  L R+   CP++ T   + D+      L            K+++ CP +
Sbjct: 118 SYLQKLGLGEGKLKRVLYCCPEIFTMR-QQDINDTVRLLKEKCLFTVQQVTKILHSCPSV 176

Query: 159 LTSSARDQLKPALFYLQ----RLGFKDLNALAYQDSVLLVSKVENTLIPKLKYLESIG 212
           L    R+ L    +  Q    R+G K  + +  +     ++K++   I    YLE +G
Sbjct: 177 L----REDLGQLEYKFQYAYFRMGIKHPDIVKSEYLQYSLTKIKQRHI----YLERLG 226


  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    0.138    0.400 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,635,149
Number of Sequences: 62578
Number of extensions: 273886
Number of successful extensions: 547
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 541
Number of HSP's gapped (non-prelim): 12
length of query: 308
length of database: 14,973,337
effective HSP length: 99
effective length of query: 209
effective length of database: 8,778,115
effective search space: 1834626035
effective search space used: 1834626035
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: 51 (24.3 bits)