BLASTP 2.2.21 [Jun-14-2009]

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= 0022.0010.p         (153 letters)

Database: COGmodified 
           192,987 sequences; 59,019,183 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

PA2426 [K] COG1595 DNA-directed RNA polymerase specialized sigma...   139   3e-33
SMc04203 [K] COG1595 DNA-directed RNA polymerase specialized sig...    83   2e-16
PA2387 [K] COG1595 DNA-directed RNA polymerase specialized sigma...    74   9e-14
PA1300 [K] COG1595 DNA-directed RNA polymerase specialized sigma...    74   1e-13
PA0472 [K] COG1595 DNA-directed RNA polymerase specialized sigma...    74   1e-13

>PA2426 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Pae Pseudomonas aeruginosa
          Length = 187

 Score =  139 bits (349), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 73/144 (50%), Positives = 93/144 (64%), Gaps = 1/144 (0%)

Query: 1   VATRILGCPHRADDVVQDTFIKIAEVPD-DFDIKQPVAYLYRIVRNLAIDRHRRSAFECD 59
           +A RI GC  RA+DVVQD F ++   P      K  ++YL++IVRNLAID +R+ A E  
Sbjct: 28  IAARITGCRSRAEDVVQDAFFRLQSAPQITSSFKAQLSYLFQIVRNLAIDHYRKQALEQK 87

Query: 60  VFTEEEDGLDVHQEGDSPEAIAISRQYLSMIGRALEGLPARTRRAFELYRLSGLTQREIA 119
               EE+GL+V  +G SPE   I+   L  I  AL  LP RTR AFE+YRL G+ Q++IA
Sbjct: 88  YSGPEEEGLNVVIQGASPETSHINYATLEHIADALTELPKRTRYAFEMYRLHGVPQKDIA 147

Query: 120 AELNISTTLVNFMIRDALACCRNL 143
            EL +S TLVNFMIRDAL  CR +
Sbjct: 148 KELGVSPTLVNFMIRDALVHCRKV 171


>SMc04203 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Sme Sinorhizobium meliloti
          Length = 159

 Score = 83.2 bits (204), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 53/149 (35%), Positives = 83/149 (55%), Gaps = 6/149 (4%)

Query: 2   ATRILGCPHRADDVVQDTFIK-IAEVPDDFDIKQPVAYLYRIVRNLAIDRHRRSAFECDV 60
           A  +LG    A+D+VQD +++ + E  D+     P  YL+RIVRNL+ ++  R   E +V
Sbjct: 13  AAPLLGSKDDAEDIVQDAYLRFVRETADEH--MPPKTYLFRIVRNLSFNKRSRRKLENNV 70

Query: 61  FTEEED--GLDVHQEGDSPEAIAISRQYLSMIGRALEGLPARTRRAFELYRLSGLTQREI 118
             E  D     + Q  ++PEA  +  +    + +AL  LP R RRAFELYR  G T ++I
Sbjct: 71  -VESADIPWWALPQAVETPEAQFLMSEAADRVAQALGALPDRMRRAFELYRFEGSTLKDI 129

Query: 119 AAELNISTTLVNFMIRDALACCRNLLQNE 147
           A EL+IS    + ++RDA+   +  L ++
Sbjct: 130 AEELSISIPTAHRLVRDAMEHLKAGLDHD 158


>PA2387 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Pae Pseudomonas aeruginosa
          Length = 159

 Score = 74.3 bits (181), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 49/126 (38%), Positives = 68/126 (53%), Gaps = 9/126 (7%)

Query: 20  FIKIAEVPDDFDIKQPVAYLYRIVRNLAIDRHRRS----AFECDVFTEEEDGLDVHQEGD 75
           ++++ E      I+ P A+LYR   NLA+D HRRS    A   +V  +EE GL       
Sbjct: 30  YLRVLERSSQAQIEHPKAFLYRTALNLAVDEHRRSRVRRAEPLEVLDDEE-GL----ASP 84

Query: 76  SPEAIAISRQYLSMIGRALEGLPARTRRAFELYRLSGLTQREIAAELNISTTLVNFMIRD 135
           SP+ +    Q L  + RAL  LPA  R +F L +L GL+  +IA  LNIS +LV   I +
Sbjct: 85  SPQTVVDQGQRLDNLQRALAELPAICRSSFLLRKLDGLSHSQIAEHLNISRSLVEKHIVN 144

Query: 136 ALACCR 141
           A+  CR
Sbjct: 145 AMKHCR 150


>PA1300 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Pae Pseudomonas aeruginosa
          Length = 175

 Score = 74.3 bits (181), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 48/142 (33%), Positives = 70/142 (49%), Gaps = 3/142 (2%)

Query: 6   LGCPHRADDVVQDTFIKIAEVPDDFDIKQPVAYLYRIVRNLAIDRHRRS---AFECDVFT 62
           LG    A D+ QDTF +  + P    ++QP A+L++I RNL  D  RR      + D   
Sbjct: 28  LGSSADAADLAQDTFAQWLKWPGRQSVEQPRAFLFQIARNLLRDHWRRQQSRGQDLDRPA 87

Query: 63  EEEDGLDVHQEGDSPEAIAISRQYLSMIGRALEGLPARTRRAFELYRLSGLTQREIAAEL 122
             ++   +  E   P      +Q LS +  AL  LP R R AF L++  GL+Q E+A  +
Sbjct: 88  ANDEPAALEGEAAGPGERFEQQQRLSHLAAALAELPPRRREAFVLHKFDGLSQVEVAERM 147

Query: 123 NISTTLVNFMIRDALACCRNLL 144
            IS ++V   I  AL  C+  L
Sbjct: 148 GISLSMVEKHIASALLHCKRRL 169


>PA0472 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Pae Pseudomonas aeruginosa
          Length = 172

 Score = 73.9 bits (180), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 52/151 (34%), Positives = 72/151 (47%), Gaps = 12/151 (7%)

Query: 3   TRILGCPHRADDVVQDTFIKIAEVPDDFDIKQPVAYLYRIVRNLAIDRHRRSAFECDVFT 62
            R LGC  RA+D+ QDTF+++   P+   +++P A+L ++ R L ID  RR+A E     
Sbjct: 28  NRNLGCRQRAEDLSQDTFVRLLGRPELPGLREPRAFLAKVARGLMIDHFRRAALEQAYLA 87

Query: 63  EEEDGLDVHQEGDSPEAIAISRQYLSM-----IGRALEGLPARTRRAFELYRLSGLTQRE 117
           E    L +  E + P A     QYL +     I R L  L  + R AF   RL G+   E
Sbjct: 88  E----LALVPEAEQPSA---EEQYLILEDLREIDRLLGTLSLKARSAFLYSRLDGMPHAE 140

Query: 118 IAAELNISTTLVNFMIRDALACCRNLLQNEP 148
           IA  L +S   V   +   L  C   L  EP
Sbjct: 141 IAERLGVSVPRVRQYLAQGLRQCYIALYGEP 171