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= 045903
         (385 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 = 40.0 bits (92), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 37/150 (24%), Positives = 68/150 (45%), Gaps = 7/150 (4%)

Query: 151 LCKAIVRNPSLLTYDLDKTIKPVVALYEQVGISRHDLIPMLMSRPTLIPRTSLN-DQKME 209
           L   + +N ++ + DL+  +K  VA       S+ D+  M+   P L+  +    D ++ 
Sbjct: 58  LGAFLTKNHAIFSEDLE-NLKTRVAYLHSKNFSKADVAQMVRKAPFLLNFSVERLDNRLG 116

Query: 210 YISRTQVSRASKMYKYVVTL--IAISRIETIRE--KVANLEKFGMSEDEIWSLFGRSPLL 265
           +  +       K    VV L  +    +E ++E  KV  LE  G   +EI  +  R P +
Sbjct: 117 FFQKELELSVKKTRDLVVRLPRLLTGSLEPVKENMKVYRLE-LGFKHNEIQHMITRIPKM 175

Query: 266 LTLSVDKVQRNMTFVVGTMKMPANVILEYP 295
           LT +  K+     FV   M +P ++I+++P
Sbjct: 176 LTANKMKLTETFDFVHNVMSIPHHIIVKFP 205


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

 Score = 39.7 bits (91), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 37/150 (24%), Positives = 68/150 (45%), Gaps = 7/150 (4%)

Query: 151 LCKAIVRNPSLLTYDLDKTIKPVVALYEQVGISRHDLIPMLMSRPTLIPRTSLN-DQKME 209
           L   + +N ++ + DL+  +K  VA       S+ D+  M+   P L+  +    D ++ 
Sbjct: 86  LGAFLTKNHAIFSEDLE-NLKTRVAYLHSKNFSKADVAQMVRKAPFLLNFSVERLDNRLG 144

Query: 210 YISRTQVSRASKMYKYVVTL--IAISRIETIRE--KVANLEKFGMSEDEIWSLFGRSPLL 265
           +  +       K    VV L  +    +E ++E  KV  LE  G   +EI  +  R P +
Sbjct: 145 FFQKELELSVKKTRDLVVRLPRLLTGSLEPVKENMKVYRLE-LGFKHNEIQHMITRIPKM 203

Query: 266 LTLSVDKVQRNMTFVVGTMKMPANVILEYP 295
           LT +  K+     FV   M +P ++I+++P
Sbjct: 204 LTANKMKLTETFDFVHNVMSIPHHIIVKFP 233


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

 Score = 32.3 bits (72), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 25/120 (20%), Positives = 53/120 (44%), Gaps = 10/120 (8%)

Query: 74  GCSDSDITKLFARRPTLQKADALNLRFKLSVLNELGLNSDDLVKIINCRPRFLSSRINIC 133
           G +   +  +  + P L K   + +R + S L +LGL    L +++ C P   + R    
Sbjct: 44  GLNPEPVCVVLKKSPQLLKLPIMQMRKRSSYLQKLGLGEGKLKRVLYCCPEIFTMR---- 99

Query: 134 FEERVDFLIKLFGSR-----EMLCKAIVRNPSLLTYDLDKTIKPVVALYEQVGISRHDLI 188
            ++ ++  ++L   +     + + K +   PS+L  DL +        Y ++GI   D++
Sbjct: 100 -QQDINDTVRLLKEKCLFTVQQVTKILHSCPSVLREDLGQLEYKFQYAYFRMGIKHPDIV 158


>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 = 31.6 bits (70), Expect = 0.85,   Method: Compositional matrix adjust.
 Identities = 25/120 (20%), Positives = 53/120 (44%), Gaps = 10/120 (8%)

Query: 74  GCSDSDITKLFARRPTLQKADALNLRFKLSVLNELGLNSDDLVKIINCRPRFLSSRINIC 133
           G +   +  +  + P L K   + +R + S L +LGL    L +++ C P   + R    
Sbjct: 89  GLNPEPVCVVLKKSPQLLKLPIMQMRKRSSYLQKLGLGEGKLKRVLYCCPEIFTMR---- 144

Query: 134 FEERVDFLIKLFGSR-----EMLCKAIVRNPSLLTYDLDKTIKPVVALYEQVGISRHDLI 188
            ++ ++  ++L   +     + + K +   PS+L  DL +        Y ++GI   D++
Sbjct: 145 -QQDINDTVRLLKEKCLFTVQQVTKILHSCPSVLREDLGQLEYKFQYAYFRMGIKHPDIV 203


>pdb|1PSW|A Chain A, Structure Of E. Coli Adp-Heptose Lps Heptosyltransferase
           Ii
          Length = 348

 Score = 30.4 bits (67), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 33/68 (48%), Gaps = 7/68 (10%)

Query: 131 NICFEERVDFLIKLFGSREMLCKAIVRNPSLLTYDLDKTIKPVVALYEQVGISRHDLIPM 190
           N+  E ++D  + L  +    CKAIV N S L +      +P+VALY   G S  D  P 
Sbjct: 245 NLAGETQLDQAVILIAA----CKAIVTNDSGLXHVAAALNRPLVALY---GPSSPDFTPP 297

Query: 191 LMSRPTLI 198
           L  +  +I
Sbjct: 298 LSHKARVI 305


>pdb|4IL3|A Chain A, Crystal Structure Of S. Mikatae Ste24p
 pdb|4IL3|B Chain B, Crystal Structure Of S. Mikatae Ste24p
          Length = 461

 Score = 28.5 bits (62), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 13/44 (29%), Positives = 25/44 (56%)

Query: 113 DDLVKIINCRPRFLSSRINICFEERVDFLIKLFGSREMLCKAIV 156
           +DL+  + C  +F+ S I+   E + D   K  G ++ LC+A++
Sbjct: 368 NDLLTPLECAMQFIMSLISRTHEYQADAYAKKLGYKQNLCRALI 411


  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    0.136    0.387 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,769,889
Number of Sequences: 62578
Number of extensions: 351249
Number of successful extensions: 694
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 689
Number of HSP's gapped (non-prelim): 14
length of query: 385
length of database: 14,973,337
effective HSP length: 101
effective length of query: 284
effective length of database: 8,652,959
effective search space: 2457440356
effective search space used: 2457440356
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: 52 (24.6 bits)