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= 0101.0017.p (185 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 2,715,099 sequences; 757,237,578 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gb|AAK94006.1| alternative sigma factor AlgU [Pseudomonas fluore... 88 8e-17 ref|NP_743585.1| RNA polymerase sigma-H factor AlgT [Pseudomonas... 87 2e-16 ref|ZP_00185746.1| hypothetical protein Rxyl351901 [Rubrobacter ... 86 4e-16 gb|AAF01335.1| alternate sigma factor AlgT [Pseudomonas syringae... 84 1e-15 ref|NP_881065.1| RNA polymerase sigma factor [Bordetella pertuss... 84 2e-15 >gb|AAK94006.1| alternative sigma factor AlgU [Pseudomonas fluorescens] Length = 193 Score = 88.2 bits (217), Expect = 8e-17, Method: Compositional matrix adjust. Identities = 60/179 (33%), Positives = 91/179 (50%), Gaps = 14/179 (7%) Query: 3 EDNELMARVQAGDKGAYEELVLKHRLKAIAFANSFVCDLYTAEDIVQECFVXXXXXYIHR 62 ED +L+ RVQ GDK A++ LVLK++ K + FV D + A+D+ QE F+ Y Sbjct: 6 EDQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTHEAQDVAQEAFI---KAYRAL 62 Query: 63 ETYQPSHAFNTYLFTIIRNSCIDYLRSRQASRSFSSEAVPE----------LSDHTTPEE 112 ++ AF T+L+ I N+ +YL SR R S+ E L D +PE Sbjct: 63 GNFRGDSAFYTWLYRIAINTAKNYLVSR-GRRPPDSDVSSEDAEFYDGDHGLKDLESPER 121 Query: 113 ILASRENTKLIYEVLDDLQIDYKTALYLYAVADFSYKDIASIMKKSVPQIKILLYRARK 171 L E ++ + L D +TAL L SY+DIAS+M+ V ++ ++RAR+ Sbjct: 122 ALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRARE 180 >ref|NP_743585.1| RNA polymerase sigma-H factor AlgT [Pseudomonas putida KT2440] gb|AAN67049.1| RNA polymerase sigma-H factor AlgT [Pseudomonas putida KT2440] Length = 193 Score = 86.7 bits (213), Expect = 2e-16, Method: Compositional matrix adjust. Identities = 59/179 (32%), Positives = 91/179 (50%), Gaps = 14/179 (7%) Query: 3 EDNELMARVQAGDKGAYEELVLKHRLKAIAFANSFVCDLYTAEDIVQECFVXXXXXYIHR 62 ED +L+ RVQ GD+ A++ LVLK++ K + FV D + A+D+ QE F+ Y Sbjct: 6 EDQQLVERVQRGDRRAFDLLVLKYQHKILGLIVRFVHDTHEAQDVAQEAFI---KAYRAL 62 Query: 63 ETYQPSHAFNTYLFTIIRNSCIDYLRSRQASRSFSSEAVPE----------LSDHTTPEE 112 ++ AF T+L+ I N+ +YL SR R S+ E L D +PE Sbjct: 63 GNFRGDSAFYTWLYRIAINTAKNYLVSR-GRRPPDSDVSSEDAEFYDGDHGLKDLESPER 121 Query: 113 ILASRENTKLIYEVLDDLQIDYKTALYLYAVADFSYKDIASIMKKSVPQIKILLYRARK 171 L E ++ + L D +TAL L SY+DIAS+M+ V ++ ++RAR+ Sbjct: 122 SLLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRARE 180 >ref|ZP_00185746.1| hypothetical protein Rxyl351901 [Rubrobacter xylanophilus DSM 9941] Length = 202 Score = 85.9 bits (211), Expect = 4e-16, Method: Compositional matrix adjust. Identities = 57/168 (33%), Positives = 81/168 (48%), Gaps = 5/168 (2%) Query: 3 EDNELMARVQAGDKGAYEELVLKHRLKAIAFANSFVCDLYTAEDIVQECFVXXXXXYIHR 62 ED EL+AR AGD +YEELV ++ + + + ED+VQE F+ Y Sbjct: 28 EDKELVARTLAGDMRSYEELVRRYERLVASLLYPYARREISVEDLVQETFL---RAYDRL 84 Query: 63 ETYQPSHAFNTYLFTIIRNSCIDYLRSRQASRSFSSEAVPELSDHTTPEEILASRENTKL 122 ET+ P + F T+L I N +D LR R+ F+ E + PE S E + Sbjct: 85 ETFNPEYRFKTWLLAIANNLGVDTLRRRREVVEFNHEV--HAGETGGPEAAALSAERAES 142 Query: 123 IYEVLDDLQIDYKTALYLYAVADFSYKDIASIMKKSVPQIKILLYRAR 170 + E + L Y L L + SY +IA +M SVP +K L+RAR Sbjct: 143 LREAVLSLPEQYSVPLMLRYGEEMSYAEIAEVMGLSVPAVKSRLFRAR 190 >gb|AAF01335.1| alternate sigma factor AlgT [Pseudomonas syringae pv. syringae] Length = 193 Score = 84.0 bits (206), Expect = 1e-15, Method: Compositional matrix adjust. Identities = 59/179 (32%), Positives = 90/179 (50%), Gaps = 14/179 (7%) Query: 3 EDNELMARVQAGDKGAYEELVLKHRLKAIAFANSFVCDLYTAEDIVQECFVXXXXXYIHR 62 ED +L+ RVQ GD A++ LVLK++ K + FV D + A+D+ QE F+ Y Sbjct: 6 EDQQLVERVQRGDTRAFDLLVLKYQHKILGLIVRFVHDTHEAQDVAQEAFI---KAYRAL 62 Query: 63 ETYQPSHAFNTYLFTIIRNSCIDYLRSRQASRSFSSEAVPE----------LSDHTTPEE 112 ++ AF T+L+ I N+ +YL SR R S+ E L D +PE Sbjct: 63 GNFRGDSAFYTWLYRIAINTAKNYLVSR-GRRPPDSDVRSEDAEFYDGDHGLKDIESPER 121 Query: 113 ILASRENTKLIYEVLDDLQIDYKTALYLYAVADFSYKDIASIMKKSVPQIKILLYRARK 171 L E ++ + L D +TAL L SY+DIAS+M+ V ++ ++RAR+ Sbjct: 122 ALLRDEIEGTVHRTIQLLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRARE 180 >ref|NP_881065.1| RNA polymerase sigma factor [Bordetella pertussis Tohama I] ref|NP_885468.1| RNA polymerase sigma factor [Bordetella parapertussis 12822] ref|NP_890287.1| RNA polymerase sigma factor [Bordetella bronchiseptica RB50] emb|CAE42709.1| RNA polymerase sigma factor [Bordetella pertussis] emb|CAE38586.1| RNA polymerase sigma factor [Bordetella parapertussis] emb|CAE35726.1| RNA polymerase sigma factor [Bordetella bronchiseptica] Length = 199 Score = 83.6 bits (205), Expect = 2e-15, Method: Compositional matrix adjust. Identities = 55/189 (29%), Positives = 96/189 (50%), Gaps = 15/189 (7%) Query: 4 DNELMARVQAGDKGAYEELVLKHRLKAIAFANSFVCDLYTAEDIVQECFVXXXXXYIHRE 63 D EL+ARVQ GDK A++ LVLK++ K + + D ED+ QE F+ Y Sbjct: 7 DAELVARVQRGDKKAFDLLVLKYQRKILRLLARMIRDPAEIEDVAQEAFIKA---YRALP 63 Query: 64 TYQPSHAFNTYLFTIIRNSCIDYLRSRQASRSFSSEAVP-----------ELSDHTTPEE 112 ++ AF T+L+ I N+ ++L S R + A+ L+D +TPE Sbjct: 64 QFRGDSAFYTWLYRIAINTARNWLAS-SGRRPSAPNAIETEDGETFNETDNLTDISTPES 122 Query: 113 ILASRENTKLIYEVLDDLQIDYKTALYLYAVADFSYKDIASIMKKSVPQIKILLYRARKK 172 + A+RE + + +++L + +TA+ L + SY+DIA M + ++ ++RAR+ Sbjct: 123 MAATREIAETVNAAIEELPEELRTAIVLREIEGMSYEDIAQSMDCPIGTVRSRIFRAREA 182 Query: 173 FKLQYKELM 181 + + L+ Sbjct: 183 IASRLRPLL 191 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Posted date: Mar 24, 2004 1:53 AM Number of letters in database: 757,237,578 Number of sequences in database: 2,715,099 Lambda K H 0.321 0.134 0.376 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 2715099 Number of Hits to DB: 237,874,981 Number of extensions: 8317103 Number of successful extensions: 22555 Number of sequences better than 1.0e-05: 225 Number of HSP's gapped: 22601 Number of HSP's successfully gapped: 225 Length of query: 185 Length of database: 757,237,578 Length adjustment: 118 Effective length of query: 67 Effective length of database: 436,855,896 Effective search space: 29269345032 Effective search space used: 29269345032 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 (21.9 bits) S2: 122 (51.6 bits)