BLASTP 2.2.18 [Mar-02-2008]


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= 0001.1796.p
         (200 letters)

Database: BlastDatabases/690/690 
           3295 sequences; 1,000,347 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|134095261|ref|YP_001100336.1| RNA polymerase sigma factor Rpo...   374   e-105
gi|134094707|ref|YP_001099782.1| ECF family RNA polymerase sigma...   112   9e-27
gi|134094095|ref|YP_001099170.1| RNA polymerase sigma factor [He...    55   2e-09
gi|134096429|ref|YP_001101504.1| putative RNA polymerase sigma f...    55   2e-09

>gi|134095261|ref|YP_001100336.1| RNA polymerase sigma factor RpoE
           [Herminiimonas arsenicoxydans]
          Length = 200

 Score =  374 bits (960), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 182/200 (91%), Positives = 191/200 (95%)

Query: 1   LTTEREIDQQLVERVQRGDKKAFELLVVKYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAY 60
           +TTER+IDQ LVERVQRGDKKAFELLV+KYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAY
Sbjct: 1   MTTERDIDQLLVERVQRGDKKAFELLVIKYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAY 60

Query: 61  RALPQFRGDSAFYTWLYRIGINTAKNYLVTMGRRAPTSTEADAEEAETFDDADHLRDINT 120
           RALPQFRGDSAFYTWLYRIGINTAKNYLVT GRRAPTSTEAD EEAETFDD +HLRDINT
Sbjct: 61  RALPQFRGDSAFYTWLYRIGINTAKNYLVTQGRRAPTSTEADIEEAETFDDGEHLRDINT 120

Query: 121 PESMLATKQIAQTVNVAMEALPEELRTAITLREIEGLSYDEIADAMNCPIGTVRSRIFRA 180
           PES+LATKQIAQT+N+AME LPEELR AITLREIEGLSYDEIA +M CPIGTVRSRIFRA
Sbjct: 121 PESLLATKQIAQTLNLAMEELPEELRMAITLREIEGLSYDEIAVSMGCPIGTVRSRIFRA 180

Query: 181 REAIAEKLRPLLDTAADKRW 200
           REAI+EKLRPLLDTA DKRW
Sbjct: 181 REAISEKLRPLLDTALDKRW 200


>gi|134094707|ref|YP_001099782.1| ECF family RNA polymerase sigma
           factor [Herminiimonas arsenicoxydans]
          Length = 231

 Score =  112 bits (281), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 68/185 (36%), Positives = 108/185 (58%), Gaps = 4/185 (2%)

Query: 8   DQQLVERVQRGDKKAFELLVVKYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAYRALPQFR 67
           D ++ +R+ RGD+ AFE ++ ++ R L R    +++D AEAEDV+QEA++ AYR + +FR
Sbjct: 15  DIEIAQRIARGDQSAFEFMMRRHNRPLYRTARSILKDDAEAEDVLQEAYLLAYRNIEKFR 74

Query: 68  GDSAFYTWLYRIGINTAKNYLVTMGRRAP-TSTEADAEEAETFDDAD-HLRDINT--PES 123
           G+SA  TWL RI IN A        RRA     ++D      ++ A+ ++ +  T  PES
Sbjct: 75  GESALSTWLTRIVINEAIGRSRKSRRRAEIIRLDSDNTSPLEYEVAEVNMNEATTEQPES 134

Query: 124 MLATKQIAQTVNVAMEALPEELRTAITLREIEGLSYDEIADAMNCPIGTVRSRIFRAREA 183
                +  + +   ++ALP+  RT   LR +E +S +E++  ++ P  TVRSR FRAR  
Sbjct: 135 AALRAEARRMLERQIDALPDVFRTVFVLRALEEMSVEEVSRCLDVPEATVRSRFFRARGM 194

Query: 184 IAEKL 188
           + E L
Sbjct: 195 LREAL 199


>gi|134094095|ref|YP_001099170.1| RNA polymerase sigma factor
           [Herminiimonas arsenicoxydans]
          Length = 184

 Score = 55.5 bits (132), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 43/179 (24%), Positives = 79/179 (44%), Gaps = 23/179 (12%)

Query: 18  GDKKAFELLVVKYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAYRALPQF---RGDSAFYT 74
           GD+ A + + +   ++L+ +  R+VR +  AEDVV +AF+  +     F   RG+     
Sbjct: 20  GDEHALQRIYIHDSKRLLGVALRIVRQRHLAEDVVHDAFVSIWNKAASFDAKRGEGR--G 77

Query: 75  WLYRIGINTAKNYLVTMGRRAPTSTEADAEEAETFDDADHLRDINTPESMLATKQIAQTV 134
           W+Y +  + A N L    R             E + D D + ++      L   Q     
Sbjct: 78  WIYSVVRHHALNMLRDRDR-------------EVYADEDAIDNMQHQNQELIIDQFELND 124

Query: 135 NVA-----MEALPEELRTAITLREIEGLSYDEIADAMNCPIGTVRSRIFRAREAIAEKL 188
           ++      +  L    R +I    ++G S+ EIA  +N P+G+V++ + R   A+ E +
Sbjct: 125 SLGQLQDCLSHLDSAKRNSILCAYVDGCSHSEIAQRLNAPLGSVKAWVKRGLAALRECM 183


>gi|134096429|ref|YP_001101504.1| putative RNA polymerase sigma
           factor [Herminiimonas arsenicoxydans]
          Length = 168

 Score = 55.5 bits (132), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 42/152 (27%), Positives = 71/152 (46%), Gaps = 14/152 (9%)

Query: 33  KLMRLVSRLVRDQAEAEDVVQEAFIKAYRALPQFRGDSAFYTWLYRIGINTAKNYLVTMG 92
           +L R    L+ ++  A+D+VQ+   + ++ L  ++  S    WL+ I      N  +   
Sbjct: 14  RLRRYARALIGERTGADDLVQDTMERGWKKLSSWQRGSDMRAWLFGI----MHNLHIDQV 69

Query: 93  RRAPTSTEADAEEAETFDDADHLRDINTPESMLATKQIAQTVNVAMEALPEELRTAITLR 152
           RR    TE         DD   L    T ++  A     + +  A+  LP E R  + L 
Sbjct: 70  RRPGIMTE-------VLDDDTPL---PTSKATQADGLEMRDLQSALATLPPEQREILLLV 119

Query: 153 EIEGLSYDEIADAMNCPIGTVRSRIFRAREAI 184
            +E +SY+E+A  +  P+GTV SR+ RAR+ +
Sbjct: 120 ALEEMSYEEVATTLGLPLGTVMSRLSRARQKL 151


  Database: BlastDatabases/690/690
    Posted date:  Apr 9, 2011  4:48 AM
  Number of letters in database: 1,000,347
  Number of sequences in database:  3295
  
Lambda     K      H
   0.319    0.132    0.366 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 3295
Number of Hits to DB: 296,177
Number of extensions: 9599
Number of successful extensions: 38
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 36
Number of HSP's successfully gapped: 4
Length of query: 200
Length of database: 1,000,347
Length adjustment: 77
Effective length of query: 123
Effective length of database: 746,632
Effective search space: 91835736
Effective search space used: 91835736
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 (21.8 bits)
S2: 126 (53.1 bits)