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= 0061.0020.p         (182 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

RSp1651 [K] COG1595 DNA-directed RNA polymerase specialized sigm...    72   6e-13
SMc04051 [K] COG1595 DNA-directed RNA polymerase specialized sig...    62   7e-10
mlr0407 [K] COG1595 DNA-directed RNA polymerase specialized sigm...    62   9e-10
alr3280 [K] COG1595 DNA-directed RNA polymerase specialized sigm...    61   1e-09
AGl1386 [K] COG1595 DNA-directed RNA polymerase specialized sigm...    59   7e-09

>RSp1651 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Rso Ralstonia solanacearum
          Length = 208

 Score = 72.0 bits (175), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 63/161 (39%), Positives = 79/161 (49%), Gaps = 24/161 (14%)

Query: 12  AQQFRDAALPCLDDAYAFAQVLMRTEADAELAVQECYRRALRRFDGLRGPAIRPWLLAIL 71
           AQ+F  A LP +D AY  A+ L     DA+  VQE   RA R F G RG   RPWLLAI+
Sbjct: 15  AQRFAQAVLPHVDAAYNLARWLCGDAQDADDIVQEACLRAFRLFGGFRGGDGRPWLLAIV 74

Query: 72  KAVCLEKLG-------QELAGENVAPERRDSAT--------------IRQL---VADLPA 107
           +     +         Q    E   P   D  T              +R+L   +A LP 
Sbjct: 75  RNTWFSECARRRQAHTQPWQDEADLPPADDLTTYGADPAALLARADDVRRLQAALARLPV 134

Query: 108 PLREVIALREMIDLSYKEIAEVTGIPVTTVMSRIAEARAML 148
             REV+ LRE+ DL Y++IA V  +PV TVMSR+A AR  L
Sbjct: 135 AYREVLVLRELEDLPYRDIAAVVDVPVGTVMSRLARARQQL 175


>SMc04051 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Sme Sinorhizobium meliloti
          Length = 178

 Score = 62.0 bits (149), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 47/135 (34%), Positives = 69/135 (51%), Gaps = 16/135 (11%)

Query: 27  YAFAQVLMRTEADAELAVQECYRRALR-RFDGLRGPAIRPWLLAILKAVCLEK------- 78
           +A+A  L R    A+   QEC  RAL  R      PA R WL AIL+ + +++       
Sbjct: 21  FAYAVALSRDRDGAQDIFQECIARALDARSVPETEPAFRAWLFAILRNIWIDQSRLRRRR 80

Query: 79  --LGQELAGE----NVAPERR--DSATIRQLVADLPAPLREVIALREMIDLSYKEIAEVT 130
             L QE   +     VAPE    D+ ++RQ    L    RE++AL ++   SY+E+A + 
Sbjct: 81  SDLEQEFVTDLVPAPVAPETVLVDAFSVRQAFTRLSTEHREILALVDISGFSYEEVAMMI 140

Query: 131 GIPVTTVMSRIAEAR 145
            +P  TVMSR++ AR
Sbjct: 141 AVPKGTVMSRVSRAR 155


>mlr0407 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Mlo Mesorhizobium loti
          Length = 183

 Score = 61.6 bits (148), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 47/136 (34%), Positives = 65/136 (47%), Gaps = 16/136 (11%)

Query: 29  FAQVLMRTEADAELAVQECYRRALRRFDGLR-GPAIRPWLLAIL-------------KAV 74
           +AQ L R  ADAE  V +   RA  R    R G  +R WLL+I+             +AV
Sbjct: 26  YAQSLTRDSADAEDLVHDALVRAYERRGTFRSGGNLRAWLLSIVHNAFIDRMRSRRSEAV 85

Query: 75  CLEKLGQELAGENVAPERRDS--ATIRQLVADLPAPLREVIALREMIDLSYKEIAEVTGI 132
            +E+ G        AP+      A +R    +LP   R  + L  +  LSY++ A  TG+
Sbjct: 86  RIEQAGYLADAATPAPQEHSVRLAQVRDAFFNLPEEQRSALHLVAIEGLSYQQAANATGV 145

Query: 133 PVTTVMSRIAEARAML 148
           P+ T+MSRI  ARA L
Sbjct: 146 PLGTLMSRIGRARAAL 161


>alr3280 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Nos Nostoc sp. PCC 7120
          Length = 218

 Score = 61.2 bits (147), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 54/168 (32%), Positives = 78/168 (46%), Gaps = 45/168 (26%)

Query: 25  DAYAFAQVLMR--TEAD-------------AELAVQECYRRALRRFDGLRGPA-IRPWLL 68
           D  AFA++L R  T+ D             A+LA QE + R  R  + L+ P+  R WL 
Sbjct: 42  DRVAFAELLRRYQTQVDRVLYHLAPDWSDRADLA-QEVWIRVYRNINRLQEPSKFRGWLS 100

Query: 69  AILKAVCLEKL-----------------------GQELAGENVAPE-----RRDSATIRQ 100
            I   +  ++L                         E+AG+   PE     R     +R+
Sbjct: 101 RIATNLFYDELRKRKRVVSPLSLDAPRSVDDGEMDWEIAGDTPGPEEELTTREFYEQLRE 160

Query: 101 LVADLPAPLREVIALREMIDLSYKEIAEVTGIPVTTVMSRIAEARAML 148
            +ADLP   R  I LRE+  ++Y+EIAE+TG+ + TV SRIA AR+ L
Sbjct: 161 AIADLPEVFRTTIVLREIEGMAYEEIAEITGVSLGTVKSRIARARSRL 208


>AGl1386 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog Atu Agrobacterium tumefaciens strain C58
           (Cereon)
          Length = 189

 Score = 58.5 bits (140), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 49/159 (30%), Positives = 76/159 (47%), Gaps = 15/159 (9%)

Query: 5   AKAGNKTAQQFRDAALPCLDDAYAFAQVLMRTEADAELAVQECYRRALRRFDGLR-GPAI 63
           AK   +T   F+   L  L +  AFA  L+R+   A+  VQ+   +A  + D  + G  +
Sbjct: 3   AKEPEQTEYNFKREMLAALPNLRAFAISLIRSRDRADDLVQDTIMKAWAKQDSFQPGTNM 62

Query: 64  RPWLLAILKAVC---LEKLGQELAGEN--------VAPERRDSATIRQL---VADLPAPL 109
           R WL+ IL+      + K G+E+   +        V PE+  S  ++     +A LP   
Sbjct: 63  RAWLVTILRNEFYSQIRKSGREVQDTDGVYTSRLSVPPEQHGSVDLQDFRTALAKLPDDQ 122

Query: 110 REVIALREMIDLSYKEIAEVTGIPVTTVMSRIAEARAML 148
           RE I L      +Y+E AE+ G PV T+ SR++ AR  L
Sbjct: 123 REAILLIGASGFAYEEAAEICGCPVGTIKSRVSRARLRL 161