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= 0012.0064.p (178 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor,... 361 e-101 gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor ... 117 8e-28 gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor,... 114 6e-27 gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor ... 103 6e-24 gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor,... 99 1e-22 >gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 178 Score = 361 bits (926), Expect = e-101, Method: Compositional matrix adjust. Identities = 178/178 (100%), Positives = 178/178 (100%) Query: 1 MSSYPISDHPPAMSRIEAIFIEHHGWLRTRLRRSVGDAFTAEDVAAETFTQLLHSPPPQE 60 MSSYPISDHPPAMSRIEAIFIEHHGWLRTRLRRSVGDAFTAEDVAAETFTQLLHSPPPQE Sbjct: 1 MSSYPISDHPPAMSRIEAIFIEHHGWLRTRLRRSVGDAFTAEDVAAETFTQLLHSPPPQE 60 Query: 61 VREPRALLTTISRRIVYELWRRRDLEEACLQALAHVSGDVQAISPEDQLQLLQALRAMDQ 120 VREPRALLTTISRRIVYELWRRRDLEEACLQALAHVSGDVQAISPEDQLQLLQALRAMDQ Sbjct: 61 VREPRALLTTISRRIVYELWRRRDLEEACLQALAHVSGDVQAISPEDQLQLLQALRAMDQ 120 Query: 121 ALAGLSAKECAAFLLYKLDGLTYQAIGAQLRITPSVARRYVAKGLLQCYKAAGFAPLE 178 ALAGLSAKECAAFLLYKLDGLTYQAIGAQLRITPSVARRYVAKGLLQCYKAAGFAPLE Sbjct: 121 ALAGLSAKECAAFLLYKLDGLTYQAIGAQLRITPSVARRYVAKGLLQCYKAAGFAPLE 178 >gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor protein [Herbaspirillum seropedicae SmR1] Length = 173 Score = 117 bits (292), Expect = 8e-28, Method: Compositional matrix adjust. Identities = 67/165 (40%), Positives = 97/165 (58%), Gaps = 1/165 (0%) Query: 7 SDHPPAMSRIEAIFIEHHGWLRTRLRRSVGDAFTAEDVAAETFTQLLHSPPPQEVREPRA 66 +D P + F + WL+ LRR V AEDVA+ F ++ P +REPRA Sbjct: 9 ADQPFRHDFLVTEFTNSYSWLKQYLRRQVKSLADAEDVASAAFVEMASLPDVSIIREPRA 68 Query: 67 LLTTISRRIVYELWRRRDLEEACLQALAHVSGDVQAISPEDQLQLLQALRAMDQALAGLS 126 LLTTIS+R+V++LWRRRD EA A + + SPE L+++Q L +D+ L GLS Sbjct: 69 LLTTISQRLVFDLWRRRD-LEAAYLAALATTEEATTPSPEVVLEVVQTLVNIDRLLYGLS 127 Query: 127 AKECAAFLLYKLDGLTYQAIGAQLRITPSVARRYVAKGLLQCYKA 171 AFL +LDGLTY+ I L ++ S+ R+Y+A+ L +CY++ Sbjct: 128 KNARQAFLYSQLDGLTYREIAELLGVSVSMVRKYIAQALAKCYES 172 >gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 174 Score = 114 bits (284), Expect = 6e-27, Method: Compositional matrix adjust. Identities = 63/162 (38%), Positives = 97/162 (59%), Gaps = 2/162 (1%) Query: 9 HPPAMSRIEAIFIEHHGWLRTRLRRSVGDAFTAEDVAAETFTQLLHSPPPQE-VREPRAL 67 H R ++ EHHGWL+ LRR VG +F A D+A +TF ++L P + VREPRA Sbjct: 5 HTVHAQRFHTLYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVLGKPGALDGVREPRAW 64 Query: 68 LTTISRRIVYELWRRRDLEEACLQALAHVSGDVQAISPEDQLQLLQALRAMDQALAGLSA 127 L+ I+ +V + RR ++E CL+A+AH+ + + +SPE +L L++AL +D L GL Sbjct: 65 LSRIAHGLVVDKLRREEVERTCLEAIAHLP-EPEVVSPEARLILVEALCMIDALLEGLGE 123 Query: 128 KECAAFLLYKLDGLTYQAIGAQLRITPSVARRYVAKGLLQCY 169 + AFLL +LD ++Y I L ++ S +Y+A + CY Sbjct: 124 RARQAFLLSRLDEMSYPEIARHLGVSLSSVEKYMAAAIRHCY 165 >gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor protein [Herbaspirillum seropedicae SmR1] Length = 181 Score = 103 bits (258), Expect = 6e-24, Method: Compositional matrix adjust. Identities = 70/162 (43%), Positives = 101/162 (62%), Gaps = 2/162 (1%) Query: 11 PAMSRIEAIFIEHHGWLRTRLRRSVGDAFTAEDVAAETFTQLLHSP-PPQEVREPRALLT 69 P IEA++ +HH WL+ L+R +G++ A D+A +TF +LL S P + EPRA LT Sbjct: 15 PVPMSIEALYCDHHSWLKGWLQRRLGNSEQAADLAQDTFLRLLGSERVPSVIHEPRAYLT 74 Query: 70 TISRRIVYELWRRRDLEEACLQALAHVSGDVQAISPEDQLQLLQALRAMDQALAGLSAKE 129 T+++R+V LWRR LE+A L+ALA + A SP++Q LL+ L +DQ L L + Sbjct: 75 TVAQRLVSNLWRREKLEQAYLEALAQAPVAL-APSPQEQAILLETLLELDQLLDELPSIV 133 Query: 130 CAAFLLYKLDGLTYQAIGAQLRITPSVARRYVAKGLLQCYKA 171 AFLL +LDGLT+ + A L I+ +RY+ K L +CY A Sbjct: 134 RRAFLLSQLDGLTHAQVAAALGISIPTVKRYLVKALQRCYFA 175 >gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 169 Score = 99.4 bits (246), Expect = 1e-22, Method: Compositional matrix adjust. Identities = 64/160 (40%), Positives = 89/160 (55%), Gaps = 1/160 (0%) Query: 12 AMSRIEAIFIEHHGWLRTRLRRSVGDAFTAEDVAAETFTQLLHSPPPQEVREPRALLTTI 71 A I ++ EHHGWL L R + D+A +TF +LL PP ++REPRA LTTI Sbjct: 10 AHQEIGGLYREHHGWLVAWLSRRLACRHLGADLAQDTFVRLLGHRPPPDLREPRAYLTTI 69 Query: 72 SRRIVYELWRRRDLEEACLQALAHVSGDVQAISPEDQLQLLQALRAMDQALAGLSAKECA 131 ++ +V RRR LE A L+ALA + Q S E++L +L L +D+ L L A+ Sbjct: 70 AKGLVASHLRRRQLETAYLEALAALPEPSQP-SAEERLLVLDTLCEIDRILDQLPARARQ 128 Query: 132 AFLLYKLDGLTYQAIGAQLRITPSVARRYVAKGLLQCYKA 171 FLL +LDGL Y +I L I+ S +R++ L C A Sbjct: 129 VFLLAQLDGLPYASIAGLLGISLSTVKRHMVLALRHCLAA 168 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.322 0.134 0.396 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 550,635 Number of extensions: 20425 Number of successful extensions: 107 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 97 Number of HSP's successfully gapped: 7 Length of query: 178 Length of database: 1,619,870 Length adjustment: 79 Effective length of query: 99 Effective length of database: 1,245,805 Effective search space: 123334695 Effective search space used: 123334695 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 (22.0 bits) S2: 127 (53.5 bits)