RPS-BLAST 2.2.16 [Mar-25-2007]

Database: 40scop73nmM 
           9549 sequences; 1,678,726 total letters

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

Query= AAZ56815.1 tfus0 AAZ56815.1 GIB00263CH01 "DNA polymerase III
delta prime subunit"
         (390 letters)



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

1jr3A2 [c.37.1.20] DNA POLYMERASE III SUBUNIT GAMMA A:3 -- 242        109   5e-27
1a5tA2 [c.37.1.20] DELTA PRIME A:1 -- 207                              60   4e-12
2fug11 [a.29.12.1] NADH-QUINONE OXIDOREDUCTASE CHAIN 1 1:334 -- 438    53   4e-10
1a5tA1 [a.80.1.1] DELTA PRIME A:208 -- 330                             49   7e-09
1iqpA2 [c.37.1.20] RFCS A:2 -- 232                                     33   6e-04

>1jr3A2 [c.37.1.20] DNA POLYMERASE III SUBUNIT GAMMA A:3 -- 242
          Length = 240

 Score =  109 bits (274), Expect = 5e-27
 Identities = 47/152 (30%), Positives = 70/152 (46%), Gaps = 5/152 (3%)

Query: 36  MTHAWLFTGPPXXXXXXXXXXXXXXLQCTHG----GCGECASCHQVLAGTHPDVLYVRPS 91
           + HA+LF+G                L C  G     CG C +C ++  G   D++ +  +
Sbjct: 35  IHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAA 94

Query: 92  GLSFGVEQTRELVVRAASSPTGGRFRVVLFEDADRATEAASNALLKAIEEPAPRTVWLLC 151
             +  VE TR+L+     +P  GRF+V L ++    +  + NALLK +EEP     +LL 
Sbjct: 95  SRT-KVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLA 153

Query: 152 TPTAHDLLVTIRSRCRLVNLRTPSTEAIIDAL 183
           T     L VTI SRC   +L+    E I   L
Sbjct: 154 TTDPQKLPVTILSRCLQFHLKALDVEQIRHQL 185


>1a5tA2 [c.37.1.20] DELTA PRIME A:1 -- 207
          Length = 207

 Score = 60.3 bits (145), Expect = 4e-12
 Identities = 53/152 (34%), Positives = 67/152 (44%), Gaps = 6/152 (3%)

Query: 38  HAWLFTGPPXXXXXXXXXXXXXXLQC----THGGCGECASCHQVLAGTHPDVLYVRPSG- 92
           HA L    P              L C     H  CG C  C  + AGTHPD   + P   
Sbjct: 25  HALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKG 84

Query: 93  -LSFGVEQTRELVVRAASSPTGGRFRVVLFEDADRATEAASNALLKAIEEPAPRTVWLLC 151
             + GV+  RE+  +       G  +VV   DA   T+AA+NALLK +EEP   T + L 
Sbjct: 85  KNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLA 144

Query: 152 TPTAHDLLVTIRSRCRLVNLRTPSTEAIIDAL 183
           T     LL T+RSRCRL  L  P  +  +  L
Sbjct: 145 TREPERLLATLRSRCRLHYLAPPPEQYAVTWL 176


>2fug11 [a.29.12.1] NADH-QUINONE OXIDOREDUCTASE CHAIN 1 1:334 -- 438
          Length = 105

 Score = 53.4 bits (128), Expect = 4e-10
 Identities = 13/107 (12%), Positives = 26/107 (24%), Gaps = 14/107 (13%)

Query: 61  LQCTHGG----CGECASCHQVLAGTHPDVLYVRPSGLSFGVEQTRELVVRAASSPTGGRF 116
              T       CG+C  C + +AG   ++     +G     +    L             
Sbjct: 9   WNLTRFYAHESCGKCTPCREGVAGFMVNLFAKIGTGQG-EEKDVENLEALLPLIEGRSF- 66

Query: 117 RVVLFEDADRATEAASNALLKAIEEPAPRTVWLLCTPTAHDLLVTIR 163
                       +AA   +  ++     + + L             R
Sbjct: 67  --------CPLADAAVWPVKGSLRHFKDQYLALAREKRPVPRPSLWR 105


>1a5tA1 [a.80.1.1] DELTA PRIME A:208 -- 330
          Length = 117

 Score = 49.4 bits (118), Expect = 7e-09
 Identities = 7/92 (7%), Positives = 20/92 (21%), Gaps = 9/92 (9%)

Query: 294 LEERQKRRATRIKRDAYDTFLMDLVAFYRDVLAIQLGASVELSTXXXXXXXXXXXXSSTP 353
                      +  +     L  L     D L       V                  +P
Sbjct: 18  PSGDWYSLLAALNHEQAPARLHWLATLLMDALKRVTNVDVP-------GLVAELANHLSP 70

Query: 354 EATLRRIDAIMECRRRI--NANVHPQIAMEAM 383
                 +  +   R ++     ++ ++ +  +
Sbjct: 71  SRLQAILGDVCHIREQLMSVTGINRELLITDL 102


>1iqpA2 [c.37.1.20] RFCS A:2 -- 232
          Length = 231

 Score = 33.0 bits (74), Expect = 6e-04
 Identities = 17/83 (20%), Positives = 38/83 (45%), Gaps = 3/83 (3%)

Query: 111 PTGGRFRVVLFEDADRATEAASNALLKAIEEPAPRTVWLLCTPTAHDLLVTIRSRCRLVN 170
             G  F+++  ++AD  T+ A  AL + +E  +    ++L    +  ++  I+SRC +  
Sbjct: 105 IGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFR 164

Query: 171 LRTPSTE---AIIDALVTRDGID 190
            R    E     +  +   +G++
Sbjct: 165 FRPLRDEDIAKRLRYIAENEGLE 187


  Database: 40scop73nmM
    Posted date:  Nov 2, 2009 11:39 AM
  Number of letters in database: 1,678,726
  Number of sequences in database:  9549
  
Lambda     K      H
   0.322    0.137    0.442 

Gapped
Lambda     K      H
   0.267   0.0543    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 9549
Number of Hits to DB: 15,779,775
Number of extensions: 1102233
Number of successful extensions: 4869
Number of sequences better than 1.0e-03: 7
Number of HSP's gapped: 4808
Number of HSP's successfully gapped: 130
Length of database: 100,000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)