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= 0188.0085.p (206 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value BH0115 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 334 5e-92 BS_sigH [K] COG1595 DNA-directed RNA polymerase specialized sigm... 326 2e-89 CAC3152 [K] COG1595 DNA-directed RNA polymerase specialized sigm... 280 9e-76 lin0275 [K] COG1595 DNA-directed RNA polymerase specialized sigm... 192 3e-49 FN1518 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 120 2e-27 >BH0115 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 217 Score = 334 bits (857), Expect = 5e-92, Method: Compositional matrix adjust. Identities = 165/204 (80%), Positives = 183/204 (89%), Gaps = 2/204 (0%) Query: 3 SEYDF--ISDEEIVEIFRGGDSGALEHLINKYRNFVRAKARSYFLIGADREDIVQEGMIG 60 S DF I D +V R GD ALE+LI+KY+NFVRAKARSYFLIGAD EDIVQEGMIG Sbjct: 10 SNLDFNQIEDVGLVNRVRNGDGAALEYLIHKYKNFVRAKARSYFLIGADHEDIVQEGMIG 69 Query: 61 LYKAIRDFKGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDR 120 LYKAIRDFKGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKP+YDE+SDR Sbjct: 70 LYKAIRDFKGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPLYDEESDR 129 Query: 121 TLMDVICGTQVLDPEELIINQEEFIGLEDKMAEILSDLERKVLMLYLDGRSYQEIAEDLK 180 TL+DV+CG++V DPEEL+INQEEF +E KM E+LSDLERKVLMLYLDGRSYQEI+ +L Sbjct: 130 TLLDVVCGSRVTDPEELLINQEEFDDIEVKMGELLSDLERKVLMLYLDGRSYQEISAELN 189 Query: 181 RHVKSIDNALQRVKRKLERYLEVR 204 RHVKSIDNALQRVKRKLERY+E++ Sbjct: 190 RHVKSIDNALQRVKRKLERYMELK 213 >BS_sigH [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 218 Score = 326 bits (835), Expect = 2e-89, Method: Compositional matrix adjust. Identities = 158/198 (79%), Positives = 181/198 (91%) Query: 8 ISDEEIVEIFRGGDSGALEHLINKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRD 67 + DE+++E GDS AL++LI KYRNFVRAKARSYFLIGADREDIVQEGMIGLYK+IRD Sbjct: 18 LEDEQVIEKVHVGDSDALDYLITKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRD 77 Query: 68 FKGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDRTLMDVIC 127 FK DKL+SFKAFAELCITRQIITAIKTATRQKHIPLNSY SLDKPI+DE+SDRTL+DVI Sbjct: 78 FKEDKLTSFKAFAELCITRQIITAIKTATRQKHIPLNSYASLDKPIFDEESDRTLLDVIS 137 Query: 128 GTQVLDPEELIINQEEFIGLEDKMAEILSDLERKVLMLYLDGRSYQEIAEDLKRHVKSID 187 G + L+PEE+IINQEEF +E KM E+LSDLERKVL+LYLDGRSYQEI+++L RHVKSID Sbjct: 138 GAKTLNPEEMIINQEEFDDIEMKMGELLSDLERKVLVLYLDGRSYQEISDELNRHVKSID 197 Query: 188 NALQRVKRKLERYLEVRD 205 NALQRVKRKLE+YLE+R+ Sbjct: 198 NALQRVKRKLEKYLEIRE 215 >CAC3152 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 212 Score = 280 bits (717), Expect = 9e-76, Method: Compositional matrix adjust. Identities = 140/195 (71%), Positives = 163/195 (83%) Query: 10 DEEIVEIFRGGDSGALEHLINKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDFK 69 DEEIV + + GD + E+LINKY NFV+ KA+SYFLIGAD+EDI QEGMIGLYKAIRDFK Sbjct: 18 DEEIVMMAKLGDEKSQEYLINKYSNFVKVKAKSYFLIGADKEDICQEGMIGLYKAIRDFK 77 Query: 70 GDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDRTLMDVICGT 129 KL+SFKAFAE+CITRQIITAIKTATRQKHIPLN+YVSL+KPIYDEDSDRTL DV+ Sbjct: 78 PIKLASFKAFAEICITRQIITAIKTATRQKHIPLNTYVSLNKPIYDEDSDRTLFDVVSSV 137 Query: 130 QVLDPEELIINQEEFIGLEDKMAEILSDLERKVLMLYLDGRSYQEIAEDLKRHVKSIDNA 189 +V DPEELII++EE + M ++LS LE +VL YL+G+SYQEIA+DL R KSIDNA Sbjct: 138 EVSDPEELIISKEEVAKIRKNMLKVLSSLEIEVLESYLEGKSYQEIAKDLDRCSKSIDNA 197 Query: 190 LQRVKRKLERYLEVR 204 LQRVKRKLE+ LE R Sbjct: 198 LQRVKRKLEKCLEKR 212 >lin0275 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 301 Score = 192 bits (488), Expect = 3e-49, Method: Compositional matrix adjust. Identities = 9/190 (4%), Positives = 33/190 (17%) Query: 13 IVEIFRGGDSGALEHLINKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDFKGDK 72 + L + + + + ++ +K Sbjct: 12 AIVGRPNVGKSTLLNKLLGQKISITSRKAQTTRHRIVGIHTEGAYQAIYVDTPGLHMEEK 71 Query: 73 LSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDRTLMDVICGTQVL 132 + + + + + + + + + + L Sbjct: 72 RAINRLMNKAASSSIGDVELVIFVVEGTRWTPDDEMVLNKLREGKAPVILAVNKVDNVQE 131 Query: 133 DPEELIINQEEFIGLEDKMAEILSDLERKVLMLYLDGRSYQEIAEDLKRHVKSIDNALQR 192 + L Q + +S + I + QR Sbjct: 132 KADLLPHLQFLASQMNFLDIVPISAETGLNVDTIAAIVRKHLPEATHHFPEDYITDRSQR 191 Query: 193 VKRKLERYLE 202 + Sbjct: 192 FMASEIIREK 201 >FN1518 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 204 Score = 120 bits (300), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 68/193 (35%), Positives = 116/193 (60%), Gaps = 7/193 (3%) Query: 18 RGGDSGALEHLINKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDFKGDKLSSFK 77 + GD+ A++ ++ +Y + A+ Y+L+GA++ED+VQEG++GL KAI+ F + SSF Sbjct: 12 QSGDNEAIDLILKEYSKLLSFNAQKYYLVGAEKEDLVQEGILGLLKAIK-FYDETKSSFS 70 Query: 78 AFAELCITRQIITAIKTATRQKHIPLNSYVS----LDKPIYDEDSDRTLMDVICGTQVLD 133 +FA LCI R++I+AI+ A QKH+ LN + L+ Y +D + + + Sbjct: 71 SFAFLCIRREMISAIRKANTQKHMVLNEALKTNAILEDSAYFDDEGHNINNYKSSES--N 128 Query: 134 PEELIINQEEFIGLEDKMAEILSDLERKVLMLYLDGRSYQEIAEDLKRHVKSIDNALQRV 193 PEE + +EE + S E++VL + G SY+EIA L +++KSIDN +QR+ Sbjct: 129 PEEAYLLKEEIEEFKKFSENNFSKFEKEVLTYLIRGYSYREIATILSKNLKSIDNTIQRI 188 Query: 194 KRKLERYLEVRDN 206 ++K E +++ +N Sbjct: 189 RKKSEEWIKEEEN 201 Database: COG Posted date: Aug 3, 2010 9:58 AM Number of letters in database: 38,378,431 Number of sequences in database: 115,334 Lambda K H 0.321 0.139 0.383 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 115334 Number of Hits to DB: 14,665,572 Number of extensions: 585671 Number of successful extensions: 2970 Number of sequences better than 1.0e-05: 19 Number of HSP's gapped: 2967 Number of HSP's successfully gapped: 19 Length of query: 206 Length of database: 38,378,431 Length adjustment: 101 Effective length of query: 105 Effective length of database: 26,729,697 Effective search space: 2806618185 Effective search space used: 2806618185 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: 113 (48.1 bits)