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= 0042.0053.p         (166 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

PA3899 [K] COG1595 DNA-directed RNA polymerase specialized sigma...    96   3e-20
PA2266 [C] COG2010 Cytochrome c, mono- and diheme variants Pae P...    95   8e-20
PA1912 [K] COG1595 DNA-directed RNA polymerase specialized sigma...    89   3e-18
fecI [K] COG1595 DNA-directed RNA polymerase specialized sigma s...    84   2e-16
PA0472 [K] COG1595 DNA-directed RNA polymerase specialized sigma...    80   1e-15

>PA3899 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Pae Pseudomonas aeruginosa
          Length = 169

 Score = 96.3 bits (238), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 58/108 (53%), Positives = 72/108 (66%), Gaps = 3/108 (2%)

Query: 58  ADLNAMARYLLSLPPRQQAAPYRYDXYLEALAALPEPSQPSAEERLLVLDTLCEIDRILD 117
           A L  +AR +L    R+Q        YLEALA+LPE   PS E R +VL+TL E+DR+LD
Sbjct: 62  AFLTTIARRVLCNHYRRQDVE---RAYLEALASLPEREVPSEETRAIVLETLVELDRLLD 118

Query: 118 QLPARARQVFLLAQLDGLPYASIAGLLGISLSTVKRHMVLALRHCLAA 165
            LP  A++ FLLAQLDGL YA IA  LGISLS+VKR+M+ A + C  A
Sbjct: 119 GLPPLAKETFLLAQLDGLGYAEIATQLGISLSSVKRYMLKAAQRCYFA 166


>PA2266 [C] COG2010 Cytochrome c, mono- and diheme variants Pae Pseudomonas
           aeruginosa
          Length = 439

 Score = 94.7 bits (234), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 46/82 (56%), Positives = 59/82 (71%), Gaps = 1/82 (1%)

Query: 2   VDGWSVPSLRNEHGGGIAGWSQADLVEFLRTGRNQYTASFGAMNDVIEDSMQYMSDADLN 61
           ++ W   SLR +H  G+  WS+ADLV FLRTGR++ +A FG M+DV+  SMQYM+DADL 
Sbjct: 219 LENWIAKSLRGDHRTGLGSWSEADLVSFLRTGRSERSAVFGGMSDVVVHSMQYMTDADLT 278

Query: 62  AMARYLLSLPPRQQA-APYRYD 82
           A+ARYL SLPP   A  P+ YD
Sbjct: 279 AIARYLKSLPPADPADQPHVYD 300


>PA1912 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Pae Pseudomonas aeruginosa
          Length = 168

 Score = 89.4 bits (220), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 46/80 (57%), Positives = 58/80 (72%)

Query: 84  YLEALAALPEPSQPSAEERLLVLDTLCEIDRILDQLPARARQVFLLAQLDGLPYASIAGL 143
           YL+ALA LPE   P  E+RL+VL+TL E+D +L  LP R RQ FLLAQ++GL Y +IA  
Sbjct: 85  YLDALANLPEDLAPPPEQRLMVLETLHEVDALLGSLPDRVRQAFLLAQIEGLKYEAIAER 144

Query: 144 LGISLSTVKRHMVLALRHCL 163
           LG+SL +VKR+M  A R CL
Sbjct: 145 LGVSLGSVKRYMQQAFRQCL 164


>fecI [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Eco Escherichia coli K12
          Length = 173

 Score = 83.6 bits (205), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 56/166 (33%), Positives = 88/166 (53%), Gaps = 20/166 (12%)

Query: 6   SVPSLRNEHGGGIAGWSQADLVEFLRTGRNQYTASFGAMNDVIEDS-MQYMSDADLNAMA 64
           +  SL   H G +  W    L            ++F A +D+ +D+ ++ M    L+ + 
Sbjct: 12  TFESLYGTHHGWLKSWLTRKL-----------QSAFDA-DDIAQDTFLRVMVSETLSTIR 59

Query: 65  ---RYLLSLPPRQQAAPYRYDX----YLEALAALPEPSQPSAEERLLVLDTLCEIDRILD 117
               +L ++  R     +R +     YLE LA +PE   PS EER   L+TL  +D +LD
Sbjct: 60  DPRSFLCTIAKRVMVDLFRRNALEKAYLEMLALMPEGGAPSPEERESQLETLQLLDSMLD 119

Query: 118 QLPARARQVFLLAQLDGLPYASIAGLLGISLSTVKRHMVLALRHCL 163
            L  + R+ FLL+QLDGL Y+ IA  LG+S+S+VK+++  A+ HCL
Sbjct: 120 GLNGKTREAFLLSQLDGLTYSEIAHKLGVSISSVKKYVAKAVEHCL 165


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

 Score = 80.5 bits (197), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 41/83 (49%), Positives = 57/83 (68%)

Query: 84  YLEALAALPEPSQPSAEERLLVLDTLCEIDRILDQLPARARQVFLLAQLDGLPYASIAGL 143
           YL  LA +PE  QPSAEE+ L+L+ L EIDR+L  L  +AR  FL ++LDG+P+A IA  
Sbjct: 85  YLAELALVPEAEQPSAEEQYLILEDLREIDRLLGTLSLKARSAFLYSRLDGMPHAEIAER 144

Query: 144 LGISLSTVKRHMVLALRHCLAAL 166
           LG+S+  V++++   LR C  AL
Sbjct: 145 LGVSVPRVRQYLAQGLRQCYIAL 167