RPS-BLAST 2.2.16 [Mar-25-2007]

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

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

Query= ABO50796.1 dred0 ABO50796.1 GIB00494CH01 "RNA polymerase,
sigma-24 subunit, ECF subfamily"
         (200 letters)



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

1or7A2 [a.177.1.1] RNA POLYMERASE SIGMA-E FACTOR A:-1 -- 111           94   2e-22
1h3lA [a.177.1.1] RNA POLYMERASE SIGMA FACTOR                          86   5e-20
1iw7F3 [a.177.1.1] RNA POLYMERASE SIGMA-70 SUBUNIT F:74 -- 257         85   5e-20
1z77A2 [a.121.1.1] TRANSCRIPTIONAL REGULATOR (TETR FAMILY) A:76 ...    83   2e-19
1rp3A3 [a.177.1.1] RNA POLYMERASE SIGMA FACTOR SIGMA-28 (FLIA) A...    80   2e-18
1k78A1 [a.4.1.5] PAIRED BOX PROTEIN PAX5 A:19 -- 81                    52   5e-10
1p4wA [a.4.6.2] RCSB                                                   51   1e-09
1yioA1 [a.4.6.2] RESPONSE REGULATORY PROTEIN A:131 -- 200              50   2e-09
1ku3A [a.4.13.2] SIGMA FACTOR SIGA                                     50   2e-09
1iw7F2 [a.4.13.2] RNA POLYMERASE SIGMA-70 SUBUNIT F:319 -- 423         50   3e-09
1aw8.1 [b.52.2.1] L-ASPARTATE-ALPHA-DECARBOXYLASE A:- -- - B:- -- -    44   1e-07
1sigA [a.177.1.1] RNA POLYMERASE PRIMARY SIGMA FACTOR                  44   1e-07
1rp3A2 [a.4.13.2] RNA POLYMERASE SIGMA FACTOR SIGMA-28 (FLIA) A:...    44   2e-07
1fseA [a.4.6.2] GERE                                                   43   4e-07
1tc3C [a.4.1.2] PROTEIN (TC3 TRANSPOSASE)                              41   1e-06
1h0mA1 [a.4.6.2] TRANSCRIPTIONAL ACTIVATOR PROTEIN TRAR A:170 --...    40   2e-06
1or7A1 [a.4.13.2] RNA POLYMERASE SIGMA-E FACTOR A:120 -- 187           40   3e-06
1c9bA2 [a.74.1.2] GENERAL TRANSCRIPTION FACTOR IIB A:208 -- 316        39   5e-06
2dk5A1 [a.4.5.85] DNA-DIRECTED RNA POLYMERASE III 39 KDA A:8 -- 85     39   6e-06
1pdnC [a.4.1.5] PROTEIN (PRD PAIRED)                                   32   5e-04
1a04A1 [a.4.6.2] NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL...    32   6e-04
1fseF [a.4.6.2] GERE                                                   32   7e-04
1resA [a.4.1.2] GAMMA DELTA-RESOLVASE                                  32   8e-04

>1or7A2 [a.177.1.1] RNA POLYMERASE SIGMA-E FACTOR A:-1 -- 111
          Length = 113

 Score = 93.8 bits (233), Expect = 2e-22
 Identities = 44/93 (47%), Positives = 63/93 (67%), Gaps = 1/93 (1%)

Query: 2  PLEDQLLVERSKKGDREAFEHLVRLYENKVYTIAYRLMGNHADASDLAQDAFIKIYQALP 61
           L DQ+LVER +KGD++AF  LV  Y++KV ++  R + +  D  D+ Q+AFIK Y+AL 
Sbjct: 6  QLTDQVLVERVQKGDQKAFNLLVVRYQHKVASLVSRYVPSG-DVPDVVQEAFIKAYRALD 64

Query: 62 NFRGDSSFSTWIYHITVNVCRDELRKRQRRPTV 94
          +FRGDS+F TW+Y I VN  ++ L  + RRP  
Sbjct: 65 SFRGDSAFYTWLYRIAVNTAKNYLVAQGRRPPS 97


>1h3lA [a.177.1.1] RNA POLYMERASE SIGMA FACTOR
          Length = 75

 Score = 85.6 bits (212), Expect = 5e-20
 Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 5/77 (6%)

Query: 10 ERSKKGDREAFEHLVRLYENKVYTIAYRLMGNHADASDLAQDAFIKIYQALPNFRGDSSF 69
          ERS + +R+A E L ++Y     + A R+  N ADA DL Q+ + K Y +   FR  ++ 
Sbjct: 4  ERSARFERDALEFLDQMY-----SAALRMTRNPADAEDLVQETYAKAYASFHQFREGTNL 58

Query: 70 STWIYHITVNVCRDELR 86
            W+Y I  N   +  R
Sbjct: 59 KAWLYRILTNTFINSYR 75


>1iw7F3 [a.177.1.1] RNA POLYMERASE SIGMA-70 SUBUNIT F:74 -- 257
          Length = 184

 Score = 85.5 bits (211), Expect = 5e-20
 Identities = 16/92 (17%), Positives = 30/92 (32%), Gaps = 2/92 (2%)

Query: 1   MPLEDQLLVERSKKGDREAFEHLVRLYENKVYTIAYRLMGNHADASDLAQDAFIKIYQAL 60
              ++        +    A +HL+      V +IA +  G      DL Q+    + +A+
Sbjct: 92  SLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAV 151

Query: 61  PNFRGD--SSFSTWIYHITVNVCRDELRKRQR 90
             F       FST+            +  + R
Sbjct: 152 EKFEYKRRFKFSTYATWWIRQAINRAIADQAR 183


>1z77A2 [a.121.1.1] TRANSCRIPTIONAL REGULATOR (TETR FAMILY) A:76 --
           200
          Length = 125

 Score = 83.5 bits (206), Expect = 2e-19
 Identities = 6/95 (6%), Positives = 28/95 (29%), Gaps = 2/95 (2%)

Query: 2   PLEDQLLVERSKKGDREAFEHLVRLYENKVYTIAYRLMGNHADASDLAQDAFIKIYQALP 61
             +  + +    +G R+     +   +   +      + +   A D+ ++  +K      
Sbjct: 24  EADFLITLVSVDEGLRKRILLDLEKSQRVFFDFVREKLKDLDLAEDVTEEIALKFLXWFF 83

Query: 62  NFRGDSSFSTW--IYHITVNVCRDELRKRQRRPTV 94
           +   +    T+     +        + + +    +
Sbjct: 84  SGFEEVYLRTYQGKPELLKRDXNTLVEEVKVXLRI 118


>1rp3A3 [a.177.1.1] RNA POLYMERASE SIGMA FACTOR SIGMA-28 (FLIA)
          A:0 -- 86
          Length = 87

 Score = 80.0 bits (197), Expect = 2e-18
 Identities = 16/84 (19%), Positives = 28/84 (33%), Gaps = 5/84 (5%)

Query: 10 ERSKKGDREAFEHLVRLYENKVYTIAYRL---MGNHADASDLAQDAFIKIYQALPNFRGD 66
           ++   ++   E L+  Y   V  IA  +   +    D  DL     I + +A+ N   +
Sbjct: 2  MKNPYSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTE 61

Query: 67 --SSFSTWIYHITVNVCRDELRKR 88
                 +I         D LR  
Sbjct: 62 NPKRAEAYIKLRIKGAIYDYLRSL 85


>1k78A1 [a.4.1.5] PAIRED BOX PROTEIN PAX5 A:19 -- 81
          Length = 63

 Score = 52.1 bits (125), Expect = 5e-10
 Identities = 13/56 (23%), Positives = 19/56 (33%)

Query: 126 ETQAMIQACLNTLSDDYREIIVMREIQELAYEEIAEILGCSLGTVKSRLSRARQAL 181
                +      L D  R+ IV    Q +   +I+  L  S G V   L R  +  
Sbjct: 3   NQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETG 58


>1p4wA [a.4.6.2] RCSB
          Length = 87

 Score = 50.7 bits (121), Expect = 1e-09
 Identities = 16/81 (19%), Positives = 30/81 (37%), Gaps = 3/81 (3%)

Query: 118 PEEMLDRSETQAMIQACLNTLSDDYREIIVMREIQELAYEEIAEILGCSLGTVKSRLSRA 177
           PE +    E  +        LS    E++ +   +     EIA+ L  S+ T+ S+   A
Sbjct: 3   PESVAKLLEKISAGGYGDKRLSPKESEVLRLF-AEGFLVTEIAKKLNRSIKTISSQKKSA 61

Query: 178 RQALKEKISKQMELITPAKRL 198
              L   +   + L+     +
Sbjct: 62  MMKL--GVDNDIALLNYLSSV 80


>1yioA1 [a.4.6.2] RESPONSE REGULATORY PROTEIN A:131 -- 200
          Length = 70

 Score = 50.2 bits (120), Expect = 2e-09
 Identities = 15/64 (23%), Positives = 31/64 (48%), Gaps = 1/64 (1%)

Query: 126 ETQAMIQACLNTLSDDYREIIVMREIQELAYEEIAEILGCSLGTVKSRLSRARQALKEKI 185
           ETQ  ++   ++L+   ++++ +  I+ L  ++IA  LG +  TVK       Q L  + 
Sbjct: 1   ETQDQLEQLFSSLTGREQQVLQLT-IRGLMNKQIAGELGIAEVTVKVHRHNIMQKLNVRS 59

Query: 186 SKQM 189
              +
Sbjct: 60  LANL 63


>1ku3A [a.4.13.2] SIGMA FACTOR SIGA
          Length = 61

 Score = 50.1 bits (120), Expect = 2e-09
 Identities = 13/60 (21%), Positives = 28/60 (46%), Gaps = 4/60 (6%)

Query: 131 IQACLNTLSDDYREIIVMR----EIQELAYEEIAEILGCSLGTVKSRLSRARQALKEKIS 186
           ++  L+ LS+    ++ MR    + +E   EE+    G +   ++   ++A + LK   S
Sbjct: 2   LEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHES 61


>1iw7F2 [a.4.13.2] RNA POLYMERASE SIGMA-70 SUBUNIT F:319 -- 423
          Length = 100

 Score = 49.8 bits (119), Expect = 3e-09
 Identities = 13/76 (17%), Positives = 31/76 (40%), Gaps = 1/76 (1%)

Query: 114 NDPGPEEMLDRSETQAMIQACLNTLSDDYREIIVMREIQELAYEEIAEILGCSLGTVKSR 173
           + P P +   +S     ++  L+ LS+    ++       +  EE+    G +   ++  
Sbjct: 19  HLPSPVDAATQSLLSEELEKALSKLSEREAMVL-KLRKGLIDGEEVGAFFGVTRERIRQI 77

Query: 174 LSRARQALKEKISKQM 189
            ++A + LK   S+  
Sbjct: 78  ENKALRKLKYHESRTR 93


>1aw8.1 [b.52.2.1] L-ASPARTATE-ALPHA-DECARBOXYLASE A:- -- - B:- --
          -
          Length = 115

 Score = 44.5 bits (105), Expect = 1e-07
 Identities = 12/76 (15%), Positives = 22/76 (28%), Gaps = 4/76 (5%)

Query: 21 EHLVR--LYENKVYTIAYRLMGNHADASDLAQDAFIKIYQALPNFRGD--SSFSTWIYHI 76
            +++  L+  KV        G+ A   D    A I   +A+  +       FST+    
Sbjct: 3  RTMLQGKLHRVKVTHADLHYEGSCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAA 62

Query: 77 TVNVCRDELRKRQRRP 92
                  +       
Sbjct: 63 ERGSRIISVNGAAAHC 78


>1sigA [a.177.1.1] RNA POLYMERASE PRIMARY SIGMA FACTOR
          Length = 305

 Score = 44.1 bits (104), Expect = 1e-07
 Identities = 17/90 (18%), Positives = 33/90 (36%), Gaps = 5/90 (5%)

Query: 4   EDQLLVERSKKGDRE---AFEHLVRLYENKVYTIAYRLMGNHADASDLAQDAFIKIYQAL 60
           + + +  R   G+ +   A + +V      V +IA +         DL Q+  I + +A+
Sbjct: 216 QVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 275

Query: 61  PNF--RGDSSFSTWIYHITVNVCRDELRKR 88
             F  R    FST+            +  +
Sbjct: 276 DKFEYRRGYKFSTYATWWIRQAITRSIADQ 305


>1rp3A2 [a.4.13.2] RNA POLYMERASE SIGMA FACTOR SIGMA-28 (FLIA) A:164
           -- 234
          Length = 71

 Score = 43.6 bits (102), Expect = 2e-07
 Identities = 16/68 (23%), Positives = 36/68 (52%)

Query: 118 PEEMLDRSETQAMIQACLNTLSDDYREIIVMREIQELAYEEIAEILGCSLGTVKSRLSRA 177
            EE + + E    ++  ++ L +  + +I +   +EL  +E+A+IL  S+  V    ++A
Sbjct: 2   VEEEVIKRELTEKVKEAVSKLPEREKLVIQLIFYEELPAKEVAKILETSVSRVSQLKAKA 61

Query: 178 RQALKEKI 185
            + L+E +
Sbjct: 62  LERLREML 69


>1fseA [a.4.6.2] GERE
          Length = 67

 Score = 42.8 bits (101), Expect = 4e-07
 Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 3/64 (4%)

Query: 135 LNTLSDDYREIIVMREIQELAYEEIAEILGCSLGTVKSRLSRARQALKEKISKQMELITP 194
              L+   RE+  +  +Q+   +EIA  L  S  TV++ +S A Q L   +  + + +  
Sbjct: 2   KPLLTKREREVFELL-VQDKTTKEIASELFISEKTVRNHISNAMQKL--GVKGRSQAVVE 58

Query: 195 AKRL 198
             R+
Sbjct: 59  LLRM 62


>1tc3C [a.4.1.2] PROTEIN (TC3 TRANSPOSASE)
          Length = 51

 Score = 41.3 bits (97), Expect = 1e-06
 Identities = 7/46 (15%), Positives = 18/46 (39%)

Query: 137 TLSDDYREIIVMREIQELAYEEIAEILGCSLGTVKSRLSRARQALK 182
            LSD  R  + + ++  ++  E++  +  S   ++  L        
Sbjct: 5   ALSDTERAQLDVMKLLNVSLHEMSRKISRSRHCIRVYLKDPVSYGT 50


>1h0mA1 [a.4.6.2] TRANSCRIPTIONAL ACTIVATOR PROTEIN TRAR A:170 --
           234
          Length = 65

 Score = 40.1 bits (94), Expect = 2e-06
 Identities = 12/62 (19%), Positives = 21/62 (33%), Gaps = 3/62 (4%)

Query: 137 TLSDDYREIIVMREIQELAYEEIAEILGCSLGTVKSRLSRARQALKEKISKQMELITPAK 196
            L       +          EEIA++ G    +V+ +L  A +     +  +  L   A 
Sbjct: 4   WLDPKEATYLRWI-AVGKTXEEIADVEGVKYNSVRVKLREAXKRF--DVRSKAHLTALAI 60

Query: 197 RL 198
           R 
Sbjct: 61  RR 62


>1or7A1 [a.4.13.2] RNA POLYMERASE SIGMA-E FACTOR A:120 -- 187
          Length = 68

 Score = 39.7 bits (92), Expect = 3e-06
 Identities = 25/64 (39%), Positives = 42/64 (65%)

Query: 121 MLDRSETQAMIQACLNTLSDDYREIIVMREIQELAYEEIAEILGCSLGTVKSRLSRARQA 180
           ++   E + ++   + +L +D R  I +RE+  L+YEEIA I+ C +GTV+SR+ RAR+A
Sbjct: 2   LMLSEELRQIVFRTIESLPEDLRMAITLRELDGLSYEEIAAIMDCPVGTVRSRIFRAREA 61

Query: 181 LKEK 184
           +  K
Sbjct: 62  IDNK 65


>1c9bA2 [a.74.1.2] GENERAL TRANSCRIPTION FACTOR IIB A:208 -- 316
          Length = 109

 Score = 39.1 bits (91), Expect = 5e-06
 Identities = 8/45 (17%), Positives = 17/45 (37%)

Query: 156 YEEIAEILGCSLGTVKSRLSRARQALKEKISKQMELITPAKRLAK 200
            +EI +I G +  T++           +      +  TP  +L +
Sbjct: 64  QKEIGDIAGVADVTIRQSYRLIYPRAPDLFPTDFKFDTPVDKLPQ 108


>2dk5A1 [a.4.5.85] DNA-DIRECTED RNA POLYMERASE III 39 KDA A:8 -- 85
          Length = 78

 Score = 38.7 bits (90), Expect = 6e-06
 Identities = 2/49 (4%), Positives = 12/49 (24%), Gaps = 3/49 (6%)

Query: 131 IQACLNTLSDDYREIIVM---REIQELAYEEIAEILGCSLGTVKSRLSR 176
               +    +  + +  +      + +   ++       L  +   L  
Sbjct: 4   NAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKN 52


>1pdnC [a.4.1.5] PROTEIN (PRD PAIRED)
          Length = 123

 Score = 32.3 bits (73), Expect = 5e-04
 Identities = 11/50 (22%), Positives = 19/50 (38%)

Query: 138 LSDDYREIIVMREIQELAYEEIAEILGCSLGTVKSRLSRARQALKEKISK 187
           L ++ R  IV      +    I+  L  S G V   L+R ++    +   
Sbjct: 17  LPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 66


>1a04A1 [a.4.6.2] NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL
           A:150 -- 216
          Length = 67

 Score = 32.0 bits (73), Expect = 6e-04
 Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 3/51 (5%)

Query: 135 LNTLSDDYREIIVMREI-QELAYEEIAEILGCSLGTVKSRLSRARQALKEK 184
           +N L+   RE  +++ I Q L  + IA  L  +  TVK  +    + +K K
Sbjct: 4   VNQLTP--RERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLK 52


>1fseF [a.4.6.2] GERE
          Length = 50

 Score = 31.9 bits (73), Expect = 7e-04
 Identities = 8/45 (17%), Positives = 16/45 (35%), Gaps = 2/45 (4%)

Query: 154 LAYEEIAEILGCSLGTVKSRLSRARQALKEKISKQMELITPAKRL 198
           L   E           V++ +S A Q L   +  + + +    R+
Sbjct: 3   LTKREREVFELLVQDKVRNHISNAMQKL--GVKGRSQAVVELLRM 45


>1resA [a.4.1.2] GAMMA DELTA-RESOLVASE
          Length = 43

 Score = 31.6 bits (72), Expect = 8e-04
 Identities = 6/35 (17%), Positives = 14/35 (40%), Gaps = 1/35 (2%)

Query: 143 REIIVMREIQE-LAYEEIAEILGCSLGTVKSRLSR 176
               V+   Q+ L    I++ +  +  TV   ++ 
Sbjct: 7   DRDAVLNMWQQGLGASHISKTMNIARSTVYKVINE 41


  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
   0.323    0.139    0.424 

Gapped
Lambda     K      H
   0.267   0.0623    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 9549
Number of Hits to DB: 10,724,593
Number of extensions: 748388
Number of successful extensions: 3292
Number of sequences better than 1.0e-03: 10
Number of HSP's gapped: 3165
Number of HSP's successfully gapped: 154
Length of database: 100,000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)